Remove from pot to dry out the root(s) and soil if you can post a pic for others of both your Agave and soil

Without a photo its kinda hard to help. But you should be using a fast draining cactus putting soil. If the soil is moist I would remove the agave and allow the roots to dry before repotting.

If the main stem is damaged beyond redemption maybe try cutting it off with a sterile knife till good healthy tissue is reached, often attenuatas will regenerate from the base and throw out new pups. My regular green one developed a unhealthy top after cold damage last year, I’ve cut it off and now have several pups growing happily from the severed base. It lives in an unheated greenhouse here in the U.K. with temps as low as -8C so far and the only extra protection is from a thin horticultural fleece thrown over it and all my other plants in there. Gill

Whatever may be going on with your plants - and the photos are a bit skimpy providing that information - it is not a gnat issue. Adult fungus gnats only live for a week or so and do no feeding during this period so holes, bumps or discolored patches on the plant surface are not being caused by them. They are really just a nuisance factor only. The gnat larvae could be damaging but generally only in large numbers and only from below the soil media surface....nothing obviously visual. They also thrive in damp, organically rich environments, which also tend to be NOT the kind of growing conditions typically offered to most cacti and succulents, as they prefer a sparsely organic, more mineral based media and drier conditions. Not saying you don't have issues with fungus gnats....just that what damage you describe and what the photos attempt to indicate is not gnat related. Clearer photos - most helpful when imbedded in the text, not linked - and more details about current growing conditions could provide greater insight.