jQuery does have an option for working in a non-conflicting way but it looks like making your Exhibeo gallery use this would require substantial find-and-replace that might be more involved than simply finding-and-replacing everything.
I don’t really know a lot about Prototype and jQuery but as Jeremy suggested, you might be able to get some information from people more knowledgeable about this by reposting on the FreewayTalk list. Or someone there may know about an alternative Action to Transition FX that does play nice with Exhibeo.
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