I tried foot pedals (and still have them under my desk). They were better than nothing, but after I switched to the Kinesis Advantage keyboard I ended up not using them anymore. Hitting Ctrl+Alt with your thumbs is more convenient than hitting them with your feet, especially since I tend to fidget a lot. Another advantage (no pun intended) is that the arrow keys are convenient to hit, which lets you remap several standard Emacs keybindings. For example, I use C-b to switch buffers.
Neither switching keyboards nor using foot pedals solved my hand pain, however. I ended up having to take more drastic measures: I switched to the carpalx QGMLWB keyboard layout[1]. One of the advantages of the carpalx approach is the clear and powerful mathematical model which quantifies the effectiveness of keyboard layouts. I was able to select a layout that minimizes pinky strain--if I had switched to Dvorak or Colemak, I would have increased my pinky strain.