Week 5-6ish is quite early for harvesting. Buds are underdeveloped, trichomes nowhere near harvest ready, have never harvested that early but I now from collegues this might lead to a product with a soft and weird anxious high. I do also know the pain of bud rot from my outdoor experiments it just gets to cold and humid too early in the northern hemisphere, fast varieties and autos are a good way to go for northern outdoor growers.
When I was doing outdoor in pots I was moving them in front of a house wall with a roof overhang to finish them. A transparent roof, like u said might be a good solution. I would take the risk and check your product later on with caution. Take a scope and search for web-like formations, it's sometimes hard to spot contaminated parts with the naked eye. But since you already spotted bud rot the risk is already there. Even if you choose to chop them now you should check with high caution, smoking infected buds is extremely unhealthy