I see 2 issues.
In term of the transit, the best way to tackle that is to apply a ETA, even not require. If you are honest when applying for the ETA, the ETA result is a strong indication on your success in transit. Another alternative is to apply a physical visa, which I guess you would not like.
In term of the warrant, the best is to contact Queensland Police Service suggested by Legal Aid Queensland:
Warrants - Legal Aid Queensland
Keep in mind - just because you are transiting, it does not mean Australia can't do anything against you and has no information of your transit. In fact, another Commonwealth country has done something like this and created an massive international incident.