In hindsight players at this point should really not allow Engineers to get close enough to them in the first place but anyway, remove sprint from Engineers? That'll hamper them. (Because really, an engineer that can sprint? Super unrealistic hurrhurrhurr)
In all seriousness, maybe just tweak remote C4 damage so they only take 75% of a T2's maximum health and armour? (T1/Free Infantry will still get killed (so an engineer can still die from their own scrubby ways)
This hampers building kills as well but not too much, pretty sure most of the time there's 3-4 engineers on average make it inside a building to kill it anyway.
Additionally 1 Hotty/Techy won't be able to lonewolf a building which is also another good advantage.
Reducing the damage to remote C4s is a much easier tweak than anything else suggested, right?
Lets make suicides remove points from the team using suicide bombers.