I don't know a thing about the two drugs interating, although MMM covered that very nicely, adding excellent advice. I can speak to the Sucrafate. It will coat your stomach and help it to heal.
Even if you took just two doses of Sucrafate it would be helpful. So, as MMM said, you could take the Levothyroxine (assuming you are only to take it once a day) first thing in the morning, wait the appropriate time, then at the appropriate spaced moment, take the Sucrafate. You can at least get two, (maybe three if you're only taking Levothyroxine once a day) or even three, with one at bedtime, doses of Sucrafate.
Definitely see if a pharmacist can work up a schedule for you.
Good catch! Your doctor should have discussed this with you. It was definitely a miss for him/her.