There is hardly ever a reason why a .htaccess file needs to be so big. Most CMS can do just fine with a .htaccess file of only a dozen or two lines.
Reducing the .htaccess file size is not really about compressing it, but more about optimizing the rules so you can do more with less rules. I did a fairly in-depth analysis for this person before, maybe the tips given there help you as well:
That said, if your software really needs such a massive .htaccess file, then maybe it just isn’t possible to host it on free hosting.