It should work, however you won't be able to play vanilla without changing it back. Letting it continue with the batch file would probably be better from that standpoint.

I can't check right at the moment (about to head to work) but perhaps there might be a way to make pikes viable with out the meatgrinder "fix"?

Undertandably their secondary animations are, uhhhh, welll, basically really poor. What would happen if you gave them halberd anims and reinstituted a secondary weapon (perhaps of a spear variety assuming those get the melee handicaps from RTW)? At the very least you would probably not get the "Wanna be swordsmen" effect I think, as Halberds do seem to do a pretty fair amount of poking anyways IIRC.

I think the problem is that certain "Fixes" out there have made things worse from a balance perspectice really. Taking a unit that was cost balanced down (and perhaps anim balanced as well), hacking out a significant portion of it's code, and taking the resulting abomination as a "fix" smacks of munchkinism to me.