Running different scripts on different mIRC's is not all that uncommon. Using mIRC as a bot would be one of these situations, and also a very legitamate use of the software as well.. (as long as it isn't being used as a spam bot, as it would be just wrong to degrade your mIRC for that purpose, heh)
I agree with him that it should ask which one to load it on. I don't use IRC:// links because of this problem. I think it could handle the links more comprehensively so they will actually be more useful. At the very least, if there could be some broader option(s) to set with mIRC so that it will coordinate with other instances, such as an option for which mIRC should handle IRC:// links, it would be a definate plus.
I don't think this would be a 'terribly' difficult thing for Khaled to add either, so.. why not? (After all is said and done though, it is Khaled who has to do it, and it is his
decision). And remember.. Just because you don't run multiple instances of mIRC doesn't mean many many others don't.