Let's not overegg the paganism of Merrymount; really they were just Anglicans who elected not to go to Virginia. Not that an Anglican colony in New England isn't fascinating in itself though....
Hm. Let's assume that Morton is able to stave off Plymouth and properly develop Mount Wollaston. This is going to be a bit of a big ask; given that the majority of colonists to the region were Puritans, he's going to find it very difficult to avoid being overwhelmed by demography. In the 1630s the English authorities didn't want colonists leaving for the New World at all, and as Morton would be trying to attract Royalists I doubt he's going to have much luck; look at the difficulty Ferdinandino Gorges had in the same time period.
One interesting side effect of this, however- assuming that Merrymount lasts at least another five years or so- is that the colonisation of Massachusetts might be completely derailed. Boston is only just across the water from Morton's colony, after all; while it's possible that Winthrop wants to pick a fight and settles in the same place as OTL, he could decide to try a site on the Connecticut or Narragansett Bay instead.
I suspect that, in the best case, all of this places the Morton in the same position as Roger Williams in Rhode Island, surrounded by more populous, unfriendly Puritan neighbours. Unlike Williams, however, Morton isn't going to have any friends in England to save his bacon by giving him a colonial charter. The King is unlikely to for the reasons I mentioned above, and come the Civil War Parliament is more likely to explicitly grant the area to one of Morton's neighbours than ratify his claim.
I suspect that allowing Merrymount to survive only ensures its destruction a few years later, in more bloody circumstances; perhaps this is a TL where New England experiences something similar to Acadia's Civil War in the same period, or more likely an equivalent of Maryland's 'plundering time'.