I think Nava in LF the rest of the game is at least a wash, or maybe an upgrade (no tough lefties left for Detroit). So this isn't a an Ortiz PR situation where you have to weigh the possibility of not having Gomes later in the game. Losing Berry for a later PR situation at 1B I guess could be a small factor, but I don't think waiting for that hypothetical later in the game should be given a ton of weight over maximizing the current chances.
So to me its mostly a comparison of Gomes' base running savvy vs. Berry's extra speed. Despite the attempts to claim that with 0 outs, there aren't many ways the extra speed helps, this is just not true. The critical sac fly from 3B (or from 2nd to 3rd before the wild pitch) might happen with 0 outs. The critical single when the extra speed makes it an "automatic send" vs. "too close to call" could have happened with 0 outs. Other possibilities exist as well. You just don't know. Gomes may be faster than he looks, but Berry is significantly faster.
Quantifying Gomes baserunning intuition is more difficult, but I agree it may be a real factor (though if he was actually tagging to 3rd on the infield foul popup to Fielder I think he would have been out by 20 feet). With the pressure of the situation, and the Fenway quirks, there are some situations Gomes is probably better than Berry if he really is a better decision maker. For me, the speed difference wins out, but if you want to weigh the savvy base running more than I would, I suppose thats reasonable.
Starting Gomes vs. Scherzer in the first place was more questionable than the lack of a PR to me. Also disagreed with slow response to Clay loosing it. Not simply the lack of a hook, but the lack of a response to the situation. No one warming, no visit to the mound by Nieves to buy time, just letting it spiral out of control before giving yourself options.