Personally I don't care about people exploiting this if it makes them happy...
The biggest problem is the spam in the mission list. Why we need dozens of those missions is completely beyond me. In the time it takes me to build the mission, I could exploi... er, I mean play at least 10 of those missins myself.
Too much fuss about having 3 Emblems in 5 minutes once per day IMO. The real issue is that longer mission deserve better rewards. That's the thing that needs to be fixed. It will keep the need for the exploit down.
And if Cryptic can't put in safeguards against "grind" missions, they should instead embrace them and come up with a mission tag for Grind vs Story and have everyone's filter default to story missions. Then no one can be bothered by useless non-story missions cluttering up his mission list, Cryptic doesn'T have to add safeguards that could also annoy a story-writer, and desperate Emblem Grinders get their "free" 3 Emblems per day (and maybe their free 500 Breen kills Accolade or whatever this game has. Just also add an accolade for "500 hours played with Foundry missions" into the game.)