Well Michael Brookes has stated they "are coming" so it's safe to assume that we'll meet them at some point, whether they are currently active in the game remains to be seen.
How we interact with them depends on how closely ED lore follows the previous games.
We know first contact was around 3050, with the main invasion around 3055 and that war continues for another 140 or so years until the Thargoid invasion is halted by INRA's introduction of a Mycoid virus into the Thargoids' living machinery, at which point the Thargoids seem to disappear.
Apart from rumors, the Thargoids don't turn up again until 3252(ish) when the Allaince help them counteract the Mycoid virus and gain both a Thargoid warship and begin technological and cultural exchanges for their efforts.
So assuming ED follows this lore, then we have the unanswered question of what happened in the last 50 years to make the Thargoids disappear. The alternative being that their relationship with the Alliance remains...
Putting on a 'tin foil hat' - INRA was (is?) a Empire/Fed organisation, so when the Thargoids do return they may have a grudge to settle with both factions, at which point the Alliance may come into action as a more significant organisation.http://wiki.alioth.net/index.php/Timelinehttp://wiki.alioth.net/index.php/First_Encounters/Missions#Argent.27s_Quest_.231