Ach! You're making me cry over MY issue with this! I had bud rot on my Blackberry Moonrocks... After making some paranoid decisions, and LEARNING from them, here's what I'm going to suggest you do: Yes, cut out the rot, then spray that area with a 1% hydrogen peroxide solution (if you have 3% hydrogen peroxide, just mix 1 part of it with 2 parts water). This will kill the spores - but don't spray it so much that you're soaking it... Then you simply need to monitor your plants VERY CAREFULLY every single day to detect any other sites that may develop (and they probably will)... Examine every single bud... One plant of mine first showed it in the main cola... another plant, it showed up in one of the lowest buds... Cut them out as soon as you see them and do the spray again. And get some fans going - even outside... the fans will help reduce the humidity which is what makes this happen.
YOU are going to have to determine when you should harvest or how long you can keep her going... it's just a judgement on your part - there are no "rules" here. I thought I had ONE plant that had escaped the issue - but it didn't as I found some on her just a couple of days ago... she was close enough to harvest that I chopped her top half and it's now hanging (and btw, found a little tiny bit of rot as I was trimming her - so THAT got cut out as well and all the kief that the rot had fallen into was pitched, too...). Me, personally? I'm never growing outdoors again! Bugs, rot, foxtailing... ugh.
Good luck.... hope you can salvage a good deal of her harvest!