Hmm. I didnt know this thing was that big of an issue... It took me a few hours to figure it out...
I assumed if cavalry can have spears and swords, why cant the infantry? I searched the forums but i couldnt find anything conclusive on this matter. I started by changing in the export_descr_unit.txt file the infantry rypes, swapping the primary and secondary weapons, but didnt work. Then i thought that maybe the problem is with the skeleton changing, cause i saw that prior the ctd the unit changes weapons a few times and then the game crashes. Using a single skeleton once still crashes the game, but twice, for each weapon, it seems to work. The skeleton, as i see it, points to the animations, the game really doesnt care what the guy holds in his hands (doesnt know if it has spear or sword, only that the respective weapon has bonuses (mount_effect), is thrown and the like). Seems that if u specify spear in the stat_pri_attr line (phalanx unit style) it adds anti cav bonuses (i tested against horses, i cant say if has against chariots, camels) to the respective weapon - i read somewhere that anti cavalry bonuses may be "inherited" by secondary weapons aswell.

If im wrong, somebody correct me please, i say what i think about the game mechanics, i read little about these things, and most things i write here observed myself by trial and error.