I generally don't feel uncomfortable interviewing in a suit regardless of what they are wearing. My current job, the agent explicitly told me to wear a conservative tie, suit, polishing shoes etc and the hiring manager was in jeans. In some ways it actually makes me a little more relaxed because (rightly or wrongly) it gives me the impression they aren't going to be judging me on my appearance so I'm not say there thinking 'is my tie knot done properly?' or whatever
If you've been told to wear smart casual to the second interview then I'm not sure how this is a tough choice. Lose the jacket and tie at least.
Don't wear a suit
Smart casual for me would still involve a jacket, but would be happy in dark jeans and shoes, open neck shirt and jacket. If the interview specifies smart casual then heed it is my advice, but be on the smart side (i.e. jacket, nice shirt, shoes).
Interestingly I seen (I assume graduate) going for a role with the company a few weeks ago and was wearing a full suit with trainers. Looked smart up top but hilarious as a whole!