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I bought this golden larch from a local supermarket a couple months ago. All was well for a while, until I discovered mould at the base of the trunk (pic attached).

Drastic measures ensued, as when I cleaned it i popped it out of its pot to have a look and found an absolute state, it remained the same shape as the pot and was pretty solid. It was also COVERED in white mould. I wish I'd taken pictures but didn't even think to at the time.

I began removing all the contaminated soil and found the mould ran quite deeply into the root ball. Being a complete beginner and really not knowing what to do in this situation, I pruned it quite harshly down to healthy roots and clean soil and did give it a bit of a rinse to completely clear the mould.

I cleaned the pot thoroughly and repotted with bonsai repotting soil.

I also moved it outside at this point, in the hopes the sun would kill off any spores that might be left.

Since then, we've had a few very sunny days and the larch seemed quite happy. The past 3 days we've had some pretty heavy rain and now it's looking quite anaemic.

Help? Did I kill it?

I do not have direct experience with Larch, but what you called "mould" covering the roots within the pot, could have been mycorrhiza.

It's actually a fungus that grows in symbosis with the roots of many conifers (for sure Pines, not sure Larches) and it's quite beneficial to them, helping to absorb nutrients...

So I am afraid your larch is now suffering after the removal of the mychorriza and the heavy root pruning...

My first tought was mycorrhiza too. But also the fuzzy root tips may look like mold for some people.
After root work like this, you should keep it in a bright place with morning sun, and out of the wind for a few weeks until it recovers. For me the needles looks a bit sunburned.
When you bought it, did you keep it inside all the time, because this is a species that will lose it leaves in winter, and need a cold dormancy to stay healthy.

The problem was that you had it inside, far too wet as well. Pseudolarix amabilis is not a true larch as the name suggests, but it is treated in a similar way. Unless you are in the southern hemisphere, it should only now be in leaf, and growing. If you re potted in the green that was absolutely the wrong time to do it. Do not take it inside it needs sunlight. I don't know what you mean by anaemic, but if the leaves are yellowing that is lack of light.