There is visible rust where my left crank arm meets the bottom bracket which I believe is the cause of the creaking (only present when pedalling hard on left side).
Is it okay to spray WD40 in there to get rid of the rust?
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WD40 won't actually get rid of rust, though it will slow the rate at which it gets worse, for a little while.
However surface rust there shouldn't lead to creaking, because nothing should be moving against it, so I'd be more concerned with checking that everything is tight that should be tight, and moving parts move freely.
WD-40 is a penetrating oil. It will happily creep past the seals of the bottom bracket and thin out the grease lubricating your bottom bracket bearings. Once the grease has thinned, it won't lubricate the bearings as well, and it will want to work its way back out the same way the WD-40 got in in the first place.
You'll end up needing to repack the BB more frequently (until the WD-40 finally wears off), or you end up wearing out the BB bearings and having to replace them.
Don't spray penetrating oil near seals that hold back grease.