1) Depending on which order you're doing the missions in, you can probably get mercenary marines too.
2) Use more Medics. With units like mutalisks, you probably want more medics than 1/7, probably closer to 3.
3) Build defenses (Turrets and Bunkers). Most of the air attacks came to my first base, 1 bunker (marine, marine, firebat, marauder) 1 turret, 2 SCVs was more than enough to fend off all attacks.
Note) Reapers are nice, but they are most effective against buildings, or exploiting terrain (hitting a weak side up a cliff), they work okay in a group with marines.
Here's what I did (hard difficulty):
After initial defenses at my main base (the aforementioned bunker defenses), I got a few reapers, and traveled around the north area collecting pallets and more reapers. Running back to the medics at the base as needed.
Then, as I needed to move to other bases (heading south towards the brutalisk next), I used the provided secondary command center with 4 mercenary marines and a few medics with the 6-8 Reapers to protect it. The attacks against it were minor, but I did build a bunker and had an SCV repairing it.
I generally used this same force (3-4 medics, 4-6 mercenary marines in the bunker, 6-8 reapers) wherever I moved the command center. The reapers would jump ahead to the next mineral deposit to clear out the enemies, and run back to the medics as needed, and the rest would stay by the bunker which was just up the hill from the minerals.
I was able to completely eliminate the enemy's bases, and got the "Scenic route" achievement.