rebuild them. the kit is cheap if you have the time/tools/knowledge. the rust will clean right up (unless you are talking really, really bad) as soon as the pads hit them. if your outer pads are much more worn, maybe clean up the rotors and throw new pads on while you have it all apart to redo teh calipers. you only have 41K on a 9 year old T-100? i did alomst that much in the first year.

Scott Landon
1995 T100 - total buildup underway
1988 4Runner (22RE, W56) - new DD
2005 Dodge CTD 4x4 - Tow Beast
1990 Spec Miata
2010 GT3
2013 E92 M3