Yeah, canister filters can work with overflow towers, but are not preferable imo.
Because it's a "closed system," if you had only one tower, the tower would act as a sump, with a water level that varies with evaporation. If the water level dropped too far, then you run the risk of running your canister dry.
With two overflows (and two canisters hooked into them), all bets are off as you may run into an issue with the two towers' water level not being equal.
(I think I'm picturing this correctly....)
Removing the towers is certainly an option.. not one that I would personally do, but certainly an option if you were set on going the canister route over the sump.
I would say the biggest thing to look out for is making sure you don't mangle the caulk in the tank's seals where it intersects the seals from the overflow towers.
Don't want to mess with the seals on a 220...