It is all theory and speculation, but many have suggested that they think that the 'Far God' mentioned in Galnet entries is the Guardian AI (constructs) and that they will return sooner or later. I think it mentions in the codex that they decided to wipe out the Guardians to minimise any future threat which doesn't bode well for humans.
Personally I don't see the Thargoids as a threat and they could very well end up as an ally against any future construct attack. The Thargoids only appear to be interested in areas related to biological research and experimentation or where their materials and technology are stored. That said the more we attack them, the more chance there is of creating an enemy.
I think Mr Braben was once quoted as saying that there are worse things than Thargoids out there.
There will be others on this forum better placed to provide you with a more detailed and justified response in relation to this lore.