For anyone who is looking for an answer: Although Nathan's answer was good, yet after doing more research I noticed that non-resident F2 getting ITIN does worth nothing as F2 is not allowed to work. Also even with her having ITIN we can't file jointly (both non resident). So getting ITIN is just extra paperwork.

I called IRS to somehow disregard the filed tax return of my wife. Told them she has received a letter asking for SSN/ITIN(W7) while she wouldn't need to file the tax return in the first place, so how can I cancel/disregard the tax return. They said "Don't answer to the letter of the IRS and it's equivalent to cancellation as the further processing is not possible without your wife's SSN/ITIN requested by letter."

Hope this help someone

For anyone who is looking for an answer: Although Nathan's answer was good, after doing more research, I noticed that a non-resident F-2 getting an ITIN is worth nothing because F-2 holders are not allowed to work. Even with her having an ITIN, we can't file jointly (both non-resident). So getting an ITIN is just extra paperwork.

I called the IRS to see if they would disregard the filed tax return of my wife. I told them she has received a letter asking for SSN/ITIN(W-7), but she wouldn't need to file the tax return in the first place. So how can I cancel/disregard the tax return? They said "Don't answer the letter of the IRS and that will be equivalent to cancellation because further processing is not possible without your wife's SSN/ITIN requested by letter."