Saying Thargoids are either malevolent or benevolent is nonsense at the moment. We have no causation; only correlation, conjecture and circumstantial evidence.
The best words I have to describe the Thargoids right now is 'curious' and 'indifferent' - in equal measure.
The ship beacons merely say 'Thargoids Returned' and report about assets being lost etc.
So, if you don your trusty Science Hat of ScepticismTM* then you have to ask: if there was enough time to program a morse beacon and to hide a longer morse message in a broadcast - then why not take the time to state that it really was 'Thargoids wot did it', given the potentially disastrous ramifications of not doing so.
I'm not saying that it isn't possible that those ships were creamed by the flower/insect/barnacle-tickling Thargoids - just that there's not enough evidence to say that's definitely what happened; indeed there is as much evidence, if not more, to say that it wasn't.
Given the history, here, it's as likely, as Han Zen suggested, that the Feds picked up something they shouldn't have done, and it frappéd their systems.
Or that they were attacked by something else that made it look like Thargs.
* Available at wholesale prices from the Gnosis, Canonn Institute and Thompson Dock; and also at vastly inflated retail prices from all other Canonn stations, outposts, settlements and bases; plus many concessions in other stations throughout the bubble, the Pleiades and around Colonia