If you applied for an ITIN, that means you already filed your tax returns. Your return was filed on time. You need to wait that out. A mailed return takes 6-8 weeks. A mailed return plus an ITIN application (W7) adds several weeks to that process. The return is considered filed when you file it, not when its processed.
You don't interfere with the process by mailing a second tax return. You would also need to mail that return anyway, as you cannot efile a Married Separate return with a spouse that has no ITIN/ SSN.
When did you file the return with the ITIN application? Did you properly include a Form W7 and supporting documentation?
https://www.irs.gov/individuals/general-itin-information
