I've been jacking my GZ250s up with an ATV jack almost since day one. I the only concern about the pipes is that they are in the way. I just let it sit on them.
If your going to get one of these keep in mind that you only have 4.5 inches of ground clearance. Most of the cheaper ones are 5 inches or more tall.
I have the older version of this one.
http://www.sears.com/shc/s/p_10153_1260 ... 000P?mv=rr