The article also mentions that he immunized himself against a dozen diseases -- probably in addition to the vaccines that most Americans get in their childhood -- and quarantined himself for a while, too. He was definitely aware of the risk and tried to minimize it. Not sure whether that was enough, though. If the North Sentinelese have been isolated since the end of the last ice age, they could be vulnerable to something that outsiders don't even care about, like our normal gut flora.
Well, specifically it said he "attempted to immunize himself against 13 diseases", which isn't equivalent to actually doing that. Furthermore, I get the sense that his isolation was primarily to avoid the authorities ("he stayed not at the Lalaji but secretly—and illegally", use of the word "safehouse"), and not due to biological concerns. If anything, that was a second order benefit in his mind - "The benefit of that is that I was essentially in quarantine"...