Is it good idea to avoid choosing green side missions that reward unique allies from the current campaign, for instance, Leia Organa when playing the Return to Hoth campaign? My thinking is that sometimes these allies show up for some missions for free anyway.

No, not really. If you have not played a side mission before, it's a good choice to play.

1. You may not get to play the mission where that ally appears.

2. If you do, you don't need to pay the threat cost, and you already know how to best use that ally.

3. If the ally appears in a mission, the reward won't be to gain that ally, so you don't have a choice to take that ally to further missions.

4. If you gain a non-unique ally twice (you can't include two green side missions that grant the same ally, but it's still possible in the RtH campaign, and in campaigns with Gideon), you can use their elite version.

In a minicampaign you don't have side missions, and have other ways to earn allies.

This makes sense. Thanks!