The answer in these cases is pretty much always … sure, as long the discount is enough to make up for the amount of security you are giving to the player. How much of a discount the team needs is of course based on the risk profile of each player (both injury and performance).
I think Mookie is low risk (non-pitcher, athletic, good minor/major league track record, traditional scouting and the metrics both love him), as far as guys who only have 350 major league plate appearances go. So I would love to extend him, and don't think the Sox need as big of a discount as you'd want if you locked up a pitcher this early, especially if you get a couple team options for his first couple of FA years.
At the same time, it's entirely possible Mookie's agent knows all those things too. If Mookie's agent thinks he's 5+ WAR guy over the next 5 years, isn't interested in including any FA years, and doesn't put much value on long term security, it will be hard to come up with a deal.
Hopefully Mookie just wants to get a deal done, be set for life, and not have to think about his contract for awhile. If he puts some value on those things, an extension would be great. But if you just have to guarantee him the top of the market arb numbers in advance, and don't get any FA years included, an extension doesn't make much sense (obviously). As good as it seems like he will be, there is always a chance Mookie gets hurt or underperforms our lofty expectations.