Yes, you can, it won't hurt, but you don't have to. Since you are filing separately, you can check the box that says someone co-owns this loan and I only pay a portion of it". You will then be able to enter what portion of the loan you pay. It should then give you a drop down and will let you select that your spouses social security number is on the 1098. This will produce a statement that is attached to your return saying you share this.
In the end, if you are married filing separately, you will need to include their SSN on your return and they will have to do the same with their return. So since your name is on the 1098, and your returns will be linked, if you don't check the box, it should not create a red flag.
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