I think there is a good likelihood that plaintiffs are choosing to amend the complaint rather than fight the motion is so that they can add other claims. Remember, this lawsuit was filed at the beginning of the year and, as other people pointed out, likely a gambit made on the assumption that Axanar would fold. They didn't.
Opposing the motion to strike would just leave C/P - if they won - arguing on their original complaint and copyright infringement claims only. Think of all the things that have come to light since the beginning of the year that made so many of us go "why didn't C/P sue on THAT claim as well?" I'm not talking about alleged financial shenanigans but rather things like trademark infringement, trade dress infringement, unfair competition, use of ST motifs on coffee, potentially infringing ship designs in models sent out as perks etc.. Now that "stuff's got real", I suspect that C/P will not only amend their complaint to add specifics on the copyright claims (such as infringement in the script, in ship designs used as perks) but also to add various other counts that will open a whole new world of things defendants have to defend against. They coudl always amend their complaint later as new facts came to light (though, at a certain point, such an amendment might require permission of the court) but now they have free reign to do so early in the litigation.
M