I definitely understand the importance of maintaining mission integrity in consideration of those who came before. In the case of mission counters though, I don't see that as any real advantage over previous players' efforts/achievements such as adjusting spawn sizes/locations, number of kills, HPs, etc. would be.
I could be wrong in how I see this, maybe some will share their opinions, but newer players would still kill the same number of mobs at the same (probably higher than pre 2.0) cost, and I doubt any previous players kept killing mobs after the challenge was complete due to not having a counter.
Just my 2 cents. Regardless, I will persevere and do what I need to to complete the stage, but my OCD really wants you to consider adding some counters where they are missing.