You can prepare the return as MFJ to go along with the W7 when they request the ITIN. 

You wont be able to Efile without a SSN or ITIN.

You can e-file an MFS return without the NRA spouse's ITIN.  However, some tax software may have limitations that would not permit e-filing of these returns.  Lacerte and PTO will allow e-filing of these returns provided you have checked the box that it is an MFS return and the spouse is an NRA without an ITIN.

@Just-Lisa-Now-Have seen other PS users complaining about that.  Not a problem with Lacerte/PTO with the right box checked.

Yes, you right, Pro series won't let you print with a 1040 form with a blank in the S.S. #. It will send an error message. I think if we write in the blank area a fake number and erase it after printing it out could be a way to solve the problem.   

Will it accept NRA?

I don't use ProSeries so I don't know.