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Mercs that are part of the story line should come back on their own. I am still a bit confused, but I have found fighting on your own many times is easier than babysitting your teammates.
Resurrecting an old thread FTW!
I think I can confirm what howler noticed. It seems your Mecc comrades do have a limited number of lives. They'll make comments about needing a rest, then on the third or so down, they might make a comment about seeing a bright light, then they won't come back until the next mission or you need to retry.
One tip I'd like to add is that on the base-building levels, if you die and continue, you keep all your buildings but lose your smarties and "food". The smarties go back to where they where and the enemy frequency resets. So, in the first Mecc base fight, if you die from say, those blasted flying reapers, retry and you'll have your buildings intact, and be back to just the occasional pair of reapers. So don't think you'll have lost all that time building if you happen to not see a couple incoming RPGs.
Also, the Kabuto offspring command is different from the Mecc teammate command. Hold left control, left or right click and hold on the offspring you want to command, then aim and release on your target. They don't seem too keen on eating buildings, but they'll run some good interference for you.
Fighting Reaper Witches as Delphi: If you are low on health, hop in the water and swim away from the land. The witch will just keep hopping over you over and over. You can whittle her down by turboing at her and swiping with your sword but that takes a while.
Anyway, that's all that comes to mind for now. Pretty fun game with some silly dialog. (I love the "tears of joy" scene.)
You may also find hints and tips for the campaign from my Giants speedrun.
Youtube playlist -

Like how to kill a boss in 3 seconds. (Don't blink)

Though it also uses a few glitches from the unpatched version of the game. The most used would be "Turbo cancel" on Delphi.