If you have them available you really are better off using hardware compression set for limiting on certain tracks like Bass, Vocals and kick. You don't need to overdo it, just a fast attach and low ratio to catch potential overs. And that said even if a few overs sneak in they are often not going to ruin the recording.
You just edit them out later with a volume envelope or whatever.
Turning it way down the track will lose punch. Don't forget, the send to the computer may be digital, but Pre amps are analog and need to be driven to give out their full potential and some tone. A wimpy signal is a wimpy signal.
Your Motu was designed to make good live recordings and that's why it has the compressors built in.It's one of the reasons I was looking to buy one just for live recording.
Right now I can use my 01V as I have 6 outs from that.