The reason for this behavior is that Studio One associates instrument channels with instruments, so the channel name gets set to what the instrument tells Studio One it is. Apparently, when you select another library within Kontakt, it sort of 'resets' itself and sends it's own name to the Studio One channel. In other words, the solution you suggest would come from Native Instruments, not Presonus. I agree though, I wish, if the channel is going to take a name from the instrument, it would take the loaded library name.
I wish Studio One would provide the option of associating instrument channels with tracks, but the reason it doesn't is because Studio One doesn't really fully implement MIDI, and that might require some major code rewrites. At the very least, I wish there was an option to have the channels keep the related track names by default.