i'm just spitballing here, but i have the understanding that beer (not wort) is pretty inhospitable to anything trying to grow in it.
that being said, i don't know how that affects anything on top of the beer that's exposed to the air.
i'd scoop them out like you said, then give the beer a good smell and a little taste. if it doesn't make you gag or spit out the sip immediately, its probably fine.
fwiw, i've read that for some historical beers, a layer of mold or whatever on the top was welcome, to help keep out other beasties. but, they also believed the sun revolved around the earth at one point and look how that turned out
just out of curiosity, what kind of beer did you brew? have you experienced similar things with previous batches?