I wouldn't be so worried, tbh.
Contrary to common beliefs which (as some people might remember) I too used to hold for a very long time, the fluff of 40k has always been somewhat inconsistent and is not enforced across the franchise's various platforms. I came to realize this after long debates and careful analysis of various statements by the people who have to know:
"With Warhammer and Warhammer 40,000, the notion of canon is a fallacy. […] Warhammer and Warhammer 40,000 exist as tens of thousands of overlapping realities in the imaginations of games developers, writers, readers and gamers. None of those interpretations is wrong."
- Gav Thorpe, on his blog (http://mechanicalham...ping-the-fence/)
"It all stems from the assumption that there’s a binding contract between author and reader to adhere to some nonexistent subjective construct or ‘true’ representation of the setting. There is no such contract, and no such objective truth."
- Andy Hoare, on ADB's blog (http://www.boomtron....ii-loose-canon/)
Of course it is possible that FFG might still adopt any changes to the setting put forward by GW, either out of choice or because - for whatever reason - GW treats FFG differently and with stricter rules than it treats the Black Library. However, looking at this RPG's already existing conflicts with studio material, I don't think this is a likely outcome. Various big and small deviations make it evident that BL and FFG have always preferred to "tweak" things a little if it makes for a (subjectively) better game, depending on what they were writing at the time. What's more, a retcon as big as what is being hinted at here would invariably invalidate a lot of earlier books from FFG's RPGs - a situation that makes it somewhat attractive to simply stick to what the RPGs have established for themselves. After all, drastic changes to a setting are way more difficult to introduce in P&P RPGs that feature long and ongoing campaigns rather than the tabletop business where the majority of people's armies isn't even that fleshed out in terms of fluff and may change its face from day to day.
Worst case: Even if GW would force the issue, FFG can always opt to simply not publish anything new about the Tau and simply "forget to mention" this in any material about the Marines. It's how, according to his own words, Aaron Dembski-Bowden chose to deal with most of the stuff he doesn't like, apparently rarely contradicting it outright.
Also, there's what Adeptus-B wrote about the necessary hostility between armies.
In conclusion, I've seen way more believable rumors that turned out to be false, so … I wouldn't panic just yet.