i dunno how straight forward it would be to enable the counter, i'm no programmer, havn't been since college, i think the problem lies with the orignal mission only displaying <variable 1> the mission name, the new missions have <variable 1> & <Variable 2> which is now the counter, this means the counter is now hidden from the old mission system and i guess the problem can only be fixed when a the mission is started.
in my opinon, the only fixes i see are
1) manually update, during the VU or downtime a macro is run which is setup to copy and pase kill count from the old to new styles, and then the mission restarted with the updated totals
2) A mission terminal or the NPC tells you what your current total is (sounds like this is the route cyrene are taking) but this depends if the NPC can be set to see the progress of the mission, as currently they see if its completed or not.