Arena can do this!
Suppose a game has a time control with x minutes for y move(s). In your case you need x=2 for Komodo and x=60 for Stockfish. You achieve this by doing the following:
Go to menu Engines > Manage and in the tab Details find each engine in the left panel Installed Engines. In the right panel Selected Engine go to the tab Special and change the value for Strength(%). In your case, when starting a game with 60 minutes for 1 move, the adjusted strengths would be:
- Stockfish 100%; resulting in 1*60 minutes for 1 move
- Komodo ~3%; resulting in 0.03*60 minutes for 1 move