I don't think the Maracyn Two is negative for any healthy fish - I never had any adverse reactions. What the suggestion of isolation probably means is that the sick fish might carry over whatever his bugging him to the healthy fish. Plus, a smaller isolation tank requires less medication than a bigger tank would need.
I treat one of my ryukin for dropsy right now in a 30 gl tank, which requires more of the tablets than a 10 gl tank would be, just for example.
I wouldn't put a sick fish into a small tank like the 2.5 gl. The water quality is really a big issue with any fish, healthy or sick, but it is even more important when you treat any sick fish. Their well being depends not only on the meds, but also how good their water is. Ammonia especially would build up in such a small tank so much faster, and would add more stress to a sick fish. I'd rather treat in a bigger, filtered tank, than a too small unfiltered one.

Good luck with your ryukin - fingers are crossed....