First- make sure to find out what movements aggravate her SI and then avoid or adjust exercises that cause problems. Has she sen a doctor? Sometimes SIJ pain can actually be a disc problem that is radiating pain to the SI Joint? If she has not seen a doctor and does not have a firm diagnosis you might recommend she do so, so you can know what you are working with. Some general guidelines:
It might help you to visualize the sacrum as it lies between the 2 ilia. Think about motions that would press them into the sacrum!
Generally, with extension exercises allow her to work hip distance apart and parallel in the legs -- that is not 6 inches, just take Pilates Stance and open the heels to parallel with the large and small toes on the mat and the heels in line with the sitz bones. Avoid excessive external rotation of the hips, and make sure her Pilates Stance is coming from the 'right place' and is correctly aligned and not over rotated from the hips.
If the If she has instability with the pain, work in a ROM that she can accommodate without popping, clicking, or pain. Over time she will build strength and stability that will help.
Also make sure she has good mobility in her hips. Stiff hips can contribute to lower back pain
Finally, remember- when in doubt leave it out- and when in doubt 'refer out'. Don't be afraid to ask for help from her physical therapist (if she has one).