You’re pretty close on the sense of the sentence, but the idiom ‘come to notice’ has misled you.
Notice here is not a verb but a noun, and to is not an infinitive marker but a preposition. Come to notice might be more specifically phrased as came to the notice of the authorities or came to the notice of the intelligence services.
Come has the ‘inchoative’ sense it takes in become: it marks the beginning of an action or state. It has a passive rather than active feel—something which happened to Helene, not something which she effected—so you were closer on your first interpretation, ‘Helen had been noticed’.
Working is, as you suspect, not a gerund but a participle: a verb form acting as an adjective rather than a noun. It is not implied that her work for the DKP caused her to be noticed, merely that that is what she was doing when she was noticed—doubtless because that was where the authorities were looking.
The sentence might be paraphrased
The authorities first took notice of Helene when she was working for the German Communist Party.
Helene become an object of interest to the authorities when she was working for the German Communist Party.