I do understand the point and the reasoning. It's just rather unfortunate that the word sounds like a shortened form of Cissy or perhaps a shortened form of something else.
We're often dealing with very sensitive people, not just because they might have a problem understanding why anyone 'Would Want to Change Sex'. It's surprising how many assume that any sort of varient is by choice. Recently, I watched a discussion program on TV (I don't get out much), where someone raised the issue of Tom Robinson getting married. (The guy who wrote Glad to be Gay). Though he has made it quite clear he is a gay man who got married to a woman, (as am I), it has been portrayed widely as, this most prominent of gay activists, renouncing his allegiance and becoming normal!
I don't think we have fully appreciated the confusion that many feel. They want to understand something that they simply can't.
I have said before, here, I can't fully understand why anyone would want to reject their female gender to adopt male. (FtM) I have a reference as a transgender gmale, so I can and do, fully sympathise and empathise.
But our cisgender associates don't. So, we call these people who know they are confused and misunderstanding / not understanding, CIS
That it doesn't seem to have any derivation, just makes it seem all the more underhandedly abusive.