If a real Sofer (i.e. Orthodox) wrote a Sefer Torah for them, something I cannot understand how they can justify in the first place, I would certainly hope he pasuls it during the writing from it being a real Sefer, as the recipients will undoubtedly mistreat it in many cruel ways.
Of all the things that non-Orthodox synagogues do that don’t conform to halacha, they tend to be very good about maintaining the kavod of a sefer torah. We shouldn’t assume that they will “mistreat it in many cruel ways” just because other things they do are not correct. To the contrary, many of these congregations are very makpid to show proper kavod to their sifrei torah. Furthermore, as regards to why a sofer would write a sefer torah for a non-Orthodox congregation, consider this: The congregants in such a shul are going to not be fulfilling many mitzvos in shul, and almost certainly will not be fulfilling many mitzvos outside of shul. Shouldn’t the sofer make it possible for them to hear leyning from a kosher sefer torah? Or is it our job to deprive other Jews of the opportunity to do mitzvos just because they associate with organizations of which we don’t approve?