Considering the author's other works, and general world-views (love is a form of insanity, altruism is a falsehood, happy endings defy the laws of nature), I'm inclined to believe that this view is founded on a mix of correlation->causation fallacy, and sampling bias inherent to the genre the work is masquerading as. Essentially, you've identified two of the most obvious links between the characters, and mistakenly assumed that the writer is applying one because of the other; you've made the obvious conclusions that all the characters are female, and that their wishes lead to death and suffering, and made the erroneous logical leap that their wishes lead to suffering because they're female. To put things into the perspective of the writer, let's consider the postface of Fate/Zero Vol 1, one of his previous works.
Gen Urobuchi wants to write stories that can warm people's hearts. Those who know about my creative history will probably furrow their brows and think this is a sick joke. Honestly, I have trouble believing it myself. For when I start typing out words on the keyboard, the stories my brain comes up with are always full of madness and despair. The truth is, I haven't always been this way. I have often written pieces that didn't have a perfect ending, but by the last chapter the protagonist would still possess a belief that "Although there will be many hardships to come, I still have to hold on". But ever since I don't know when, I can no longer write works like this. I have nothing but contempt for the thing men call happiness, and have had to push the characters I poured my heart out to create into the abyss of tragedy.
Looking at his works, you see a pattern. They all have the protagonists undergo immense suffering that, from the perspective of the average viewer, is entirely undue and awful, and generally end with the heroes dying horrible deaths, which can typically be traced back to very slight character flaws, or even things that most would not consider to be flaws, such as I mentioned earlier. The reason why the characters undergo such immense suffering is, in short, because they exist in a work he penned. Now, the part which is the most interesting, especially when you consider the idea of the ending trying to justify the rest of the work...
For all things in the world, if they are just left alone and paid no attention, are bound to advance in a negative direction. No matter what we do, we can't stop the universe from getting colder, either, and on the same principle. This world is only maintained in existence by a series of logical, common-sense processes; it can never escape the bondage of its physical laws. Therefore, in order to write a perfect ending for a story you must possess the power to break the chain of cause and effect, invert black and white, and act in complete contradiction to the rules of the universe. Only a heavenly and chaste soul, a soul that resounds with genuine praise for humanity, can save the story; to write a story with a happy ending is a double challenge, to the author's body as well as the mind.
For the record, this predates PMMM. This all should sound really, really familiar, because it's pretty much a description of the goal of the Incubators, of the ending to PMMM, and of Kaname Madoka. If you make the assumption that the fact the series so strongly resembles this paragraph is not a coincidence, you can infer the following points:
1. Kaname Madoka is an idealised figure, and is based on the sort of person who pens stories with happy endings; the sort of writer Urobuchi Gen wishes he could be. 2. The ending doesn't exist to justify the story, but rather, the ending was the event around which the story was built; it would be more accurate to say the story exists to justify the ending. 3. The stories of every magical girl save Madoka are deliberately the typical sorts of stories he writes, with Kyubey filling the role of the cruel author of their fates, and Madoka being the ideal writer who, in the end, saves the story.
Now, I'm not going to get into the hilarious implications and perfect fit that is Homura representing director Shinbou Akiyuki in Rebellion, right down to forcing an ending change against the wishes of both "writers" of the story, because I've already gone on way too much of a tangent as it is, so I'll just say, in closing, the incredibly cruel treatment of the characters in the story is because this is simply how Urobuchi Gen treats the charaters of all the stories he writes.
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Looking at his works, you see a pattern. They all have the protagonists undergo immense suffering that, from the perspective of the average viewer, is entirely undue and awful, and generally end with the heroes dying horrible deaths, which can typically be traced back to very slight character flaws, or even things that most would not consider to be flaws, such as I mentioned earlier. The reason why the characters undergo such immense suffering is, in short, because they exist in a work he penned. Now, the part which is the most interesting, especially when you consider the idea of the ending trying to justify the rest of the work...
For the record, this predates PMMM. This all should sound really, really familiar, because it's pretty much a description of the goal of the Incubators, of the ending to PMMM, and of Kaname Madoka. If you make the assumption that the fact the series so strongly resembles this paragraph is not a coincidence, you can infer the following points:
Now, I'm not going to get into the hilarious implications and perfect fit that is Homura representing director Shinbou Akiyuki in Rebellion, right down to forcing an ending change against the wishes of both "writers" of the story, because I've already gone on way too much of a tangent as it is, so I'll just say, in closing, the incredibly cruel treatment of the characters in the story is because this is simply how Urobuchi Gen treats the charaters of all the stories he writes.