Among the 1,500 sources of gamma rays Fermi has mapped so

The definition of a run-on sentence is a sentence that has two or more independent clauses that aren't properly connected. Independent clauses can stand alone as separate sentences. In this sentence, you have an introductory Dependent clause (Among the...so far,) followed by an Independent clause (nothing...structures,) followed by another Dependent clause (which...Grus). Since there is only a single Independent clause this cannot be a run-on sentence.

I will admit that the sentence is awkward from a meaning standpoint. In E, the core of the sentence is only "Nothing resembles the bubble-shaped structures". "Which" is a non-essential modifier, meaning that we can leave it out of the sentence without really impacting the meaning. "That", on the other hand, is an essential modifier and needs to be part of the sentence for the sentence to make sense. I would argue that you would probably be better off with "that" instead of "which" for the final clause in this sentence, but obviously there are no valid choices using "that".

KW