Wow, you have one of the diesels! Cool beans!
Honestly, they probably never had a "plan" to remove the motor, LOL. Just stuck it in there and built around it.
I guess, you'd have to weigh the options of cutting up the floor or taking apart the cabinets.
I don't think the integrity would be compromised if you cut the flooring out, as long as the guy that reinstalls it knows what he's doing. Plus, you could have him install some reinforcing to make sure.
I'd probably vote for the cutting the floor option. That way you can just lift the motor straight out and call it a day.