Having worked with Prototype before in the past, there is no way to have it "play nice" (akin to jQuery's noConflict mode).
The very approach behind Prototype prevents this. Prototype's bread & butter comes from its Object.extend() method that gets called on objects as soon as you manipulate them with Prototype methods. Not to mention Prototype also has already modified core JavaScript objects before messing with yours.
On the other hand, jQuery is all self-contained in the jQuery object (which is, to my knowledge, all it adds to the JavaScript namespace when included).
Are there other libraries that have similar features? Sure, in fact, and I'm sure you're sick of hearing this by now, but you could probably do most of it with jQuery. However, you won't avoid the unavoidable: re-writing code. It won't be done the same way with any other framework, let alone give you the same results/beahvior.
Your choices are thus:
- Drop Prototype and re-write stuff that did use it to use something else
- Drop the third party library in favor of alternative or absence entirely
- Re-write prototype.js or thirdpartytool.js to play nicely (this, of course, is a terrible hack that will cause more headaches when you want to "upgrade" one or both tools in the future when a new release comes out)