I think you mean 48Hz, not KHz...
Yes, it is low, but it's better than interlaced isn't it? You might try adjusting brightness/contrast to improve things (if such controls are available).
Super72 (I think) might offer what you need, if you don't require lots of lines vertical resolution. As noted by the previous reply, the AGA modes should not cause any problems but, if something makes it all go horrible (even squealy sounds from the monitor and no visible picture at all) then swiftly reboot. It is very unlikely that you will cause any damage if you are quick. (My Eizo 20-50KHz multiscan did not allow normal Amiga modes at all, and made horrid shrieking sounds at 15KHz, yet still it lasted for years...)
Make sure you press Use rather than Save in the Screenmode Prefs, until you are sure that everything is ok.