Here's an answer assuming you have already sent them your scores. If not, then you don't need to do anything.
There may well not be any mechanism set up for removing information from a submitted application, but it can't hurt to ask. You should be able to find contact information for graduate admissions somewhere on the website (for example, here is where you'd find it for the Berkeley EECS department). You can send a short e-mail saying something like "I applied to [name of program] this fall and accidentally submitted GRE scores that do not properly reflect my background and accomplishments. I understand from [web page] that GRE scores are not required, so please remove them from my file. Thank you!"
They might not actually do it: just because they don't require GRE scores, it doesn't follow that they must ignore them if you submit them and then change your mind. But I don't think asking them to remove the scores will hurt your chances of admission.
I'm puzzled by the whole idea of having a strict cut-off for an optional test score. It makes me think that either the department is doing something weird or they aren't communicating clearly. In any case, though, submitting a very low score when it's optional looks weird and could hurt your application, so asking to remove the score from your application seems sensible.