Can I post a pre-print of my paper on ArXiv knowing the paper will go through major changes? Alternatives?
If you only want people who use your code to read the paper in its present form, then post it on Github with the code.  If you want a broader audience of researchers to read it in its present form, post it on arXiv.  

Updating it with substantial changes later is not a problem.  Contrary to what one of the other posted answers says, the update feature on arXiv is most commonly used to post the author's final version after peer review, which frequently contains major revisions.

I wouldn't post things to ResearchGate; to many (myself included) it is viewed mainly as a source of spam.