Hi,
If Harrison isnt playing (which he isn't) I think Colts aren't gonna win.
Is which is a relative pronoun? Yes.
Which doesn't have to refer a particular thing,right? It has to refer to something, but it does not have to be a noun. eg it can be a clause.
If it has to, where does which refer? The phrase 'Harrison isn't playing'. Please note that this type of grammar in this sentence is quite lax and informal. Don't use it when you are writing a college essay or speaking in a job interview. Another example is that 'gonna' is said, bit is only spelled thus in informal writing.
Finally, can I write this with commas?Yes.
If Harrison isn't playing, which he isn't, I think the Colts aren't gonna win.
Best wishes, Clive