i like the idea, although you will need to rebalance much stuff. you also have to either make AoE units more powerful or let AoE be capture damage(better way).
a way to avoid the massive lag that would be in a cap-only game: make some units deal real damage (ca. 50%), so you can decide between pay a little metal for damaging units (linear) or pay a bit more for cap-units (expotential)(higher risk)
@MauranKilom self-d can get turned of, so you will not self-d units which are useful for you, you will only self-d the units if you dont want to risk that a kill of your capturer will let you lose the game
next idea: make all normally built units captured by controlling com, that would be a REAL assasin mode
best idea: assasin-mode, 1/4 of all units deal hacking damage (sounds better than capture for me), some epic hack-all gameender weapons (hacking-nuke(nano-hackingdrones)), and a good risk-to-worth-to-cost ratio (also named "balance")