I am sorry, but there is not much more we can comment on this problem.
We have been looking at similar problems many times and this conflict is the most often cause of problems.
However, it is not possible to guarantee that any component will work with any template.
Booking is tested with the Joomla's default templates and there we can guarantee it shall work fine.
But if the problem is with a 3rd party template that uses JQuery and does not care about possible Mootols problems, we cannot do anything about it within Booking component.
In these cases, we can only help by providing a paid assistance with editing and fixing the problematic template -- in case you cannot resolve the problem on your own.