Yes, since you're filing as Married Filing Separate, the IRS is going to want to see her return. However, I would ask you to consider filing jointly if it results in a tax advantage. If collection of the student loan is a concern, one can file as an injured spouse.
You’re an injured spouse if your share of the refund on your joint tax return was (or is expected to be) applied against a separate past-due debt that belongs just to your spouse, with whom you filed the joint return. This can be a federal debt, state income tax debt, state unemployment compensation debt, or child or spousal support payments.
IRS Taxpayer Advocate flier Injured Spouse
To post Injured Spouse
Start at Federal
If you are filing separately due to the Income Based Repayment reduction then if she is under the filing requirement AND she has no fed/state withholding to get back then she has no reason to file HOWEVER she may want to file because the student loan folks may want to see it.
If you are not using the downloaded TT program where you can complete a second return for free then may I suggest you try one of the IRS FREE FILE options here : https://www.irs.gov/filing/free-file-do-your-federal-taxes-for-free