What you're asking to do is not a simple change; I'll leave it to Rafkos to explain re-enabling killing moves (and the bugs and performance issues that brings with it). But changing the javelin animations will require you to edit the modeldb entry for every unit affected. To identify those, look at the "soldier" line against their entry in the EDU.
Open the data\unit_models\battle_models.modeldb with Notepad++, search for the entry you need. Scroll right down to the bottom of that particular entry (eg for Euzonoi it's this):
Code:
4 None
26 EB_Fast_Short_Javelin_Prec
22 EB_Fast_ShortSwordsman
2
18 EB_Javelin_primary
14 fs_test_shield
2
18 MTW2_Sword_Primary
14 fs_test_shield
16 -0.090000004 0 0 -0.34999999 0.80000001 0.60000002
What you need to change is EB_Fast_Short_Javelin_Prec to one of the other javelin animations in the data\descr_skeleton.txt.
Repeat for every unit you want to alter - make sure you get their late models as well, for those with upgrades.