If I'm understanding this correctly, I don't think you can do what you want directly.

Best I can tell, there is nowhere for the input parameter to be set to multivalue. Even if it did, the WHERE clause would have to know if it is an "AND" or "OR" for the multivalues (obviously OR is the only one that makes sense... but someone has to code that). If you know how many multivalue inputs you have, you could just create one for each input:

On your lookup rule activity, you would just add your multivalue field for each Id input and index the token.
You could also set up a workflow like this:

I set up a multivalued "InputValues" and a multivalued "ResultValues". Then, I just run the query for each InputValue and dump out the result of the query into ResultValues. I don't think the cloud has a datarow type so if you want multiple columns returned, you would need to manage multiple ResultValue tokens.
Here's the result when I run mine:
