I'm going to answer your question with some questions:
Why do you want to switch Libraries? What are you using the separate Libraries for?
If the answer is something to the effect of: I have different types of media files (different owners, different purposes, etc), and I need them to be displayed separately, where they aren't "polluted" by other unrelated media, then... That's not what Libraries are for. You can do this in MC, quite well, all from within one Library.
It, generally, should be very rare to need to switch Libraries for most users (even ones with weird needs). JRemote does not (that I know of) expose a mechanism to switch Libraries. You could rig something up if needed, since there are commands that let you do it in MC's Media Network API (MCWS). However, where separate Libraries are most useful is when you have separate physical sets of media, which cannot be accessed simultaneously, and which require certain pre-conditions for use. For example, I have a "work" Library (the media which all lives on file shares at work, and which I cannot access from home without VPN), and a "home" Library. Another good example might be having a separate Library on a self-contained external disk, that can only be used with that disk when it is powered on and connected to a computer (and when you are using that disk, you'd never want to "switch back to" your main Library for any reason except for when you are done and unplugging it). Those kinds of usages work well.
But, having separate Libraries for my Wife and for Me, or for keeping Classical separate from Rock music, is not what they're for, and there are other (better) ways to do that.