I've never had a ganglion cyst in my foot, but I do have one in my wrist. It used to be the size of a large grape, just sticking out the top of my wrist. Since I've stopped doing pushups, it's shrunk away to nothing. As long as I don't do pushups or plank work on my hands, it stays under control. Perhaps yours will shrink away on it's own, it is definitely possible.
You might want to try icing your foot after you work out. I have a small tumor on the bottom of my foot (on the plantar fascia), and icing helps decrease the discomfort after working out.
Good Luck,
Shelbygirl