I would wate a few adys (2-3) in between the siphonings to let things get back to normal.
Are you just siphoning one small part of your tank at a time, that is what I would do. If the siphon picks out alot of sand you can lift the siphon up off the sand and slow the flow a bit. This lets the heavy sand fall beck to the sand bed and will still clean it as the small particals will stay in the siphon. If you want to do a larger area of your sand you can, just plan on doing a larger water change your corals should respond quicker also.

Bill