Your transaction should not require 3 seconds to execute. If your transaction is so complex it takes 3 seconds to execute, the chain should reject it as a denial of service attack. :P

Apply will need a short period of time during which it can make its changes, but those changes should be very fast (updating some database entries). If you're doing crazy complex, multi-millisecond computations in your smart contracts, you're probably doing it wrong, but in any event you'll need to break it up over multiple transactions because the block producers won't let you hog all the CPU time and starve out all the other users.