This is only really an issue if you don't use cave hunts (or any of the other methods) to get lots of mutant meat to bring on missions with you. Sure, they're heavy on TUs for eating, but they restore nearly an entire morale bar, usually. You can also kill the occasional enemy, just to keep morale up.
That said, I do wish there was a dedicated outfit for squad morale upkeep. You've got flags, bagpipes, and guitars, but oddly no outfit that really goes with them.