I too, have blown an ankle... twice. Both times were very bad. The number one thing you can do to heal it is get physical therapy. Shortly after your injury is the best time to induce healing in the joint, so don't let the opportunity pass. If you don't take the proper steps now, you may develop a weakness in the joint that will compound itself into hip/pelvis/lower back problems later.
That's regardless of sitting in seiza. But I think the ankle's inability to sit in seiza is a symptom of the healing that still needs to happen there. As your ankle gets stronger you'll have less and less pain sitting in seiza.
Both of my blowouts happened before I started aikido, but I have had one minor twist since. I felt that injury in my seiza for nearly a month and a half, so don't rush this one. If you are uncomfortable, change your sitting posture, and let the sensei know later. Everybody has had an issue with seiza at one point in their career.