Considering how many people enjoy playing R/S in CTF mode while complaining about people capping the flag, it seems appropriate that they should be able to switch their servers to TM and still play the same CTF maps.
That way people who enjoy R/S in different ways (being able to capture the flag vs. not) can accurately find the servers they're looking for.
It wouldn't be such a big deal to take the ctf_ off of map names, remove their flags, and wait for everyone to redownload them to play in TM; but this option adds more functionality with less work on the client's side -- a CTF map is just a two-teamed TM map with a twist, after all. It may also already be possible to force Soldat to use CTF maps in TM mode, but I'm not aware of any way to do that.