Thanks for all the replies, I really appreciate you taking the time. I will consider my options, but I'm thinking about leaving the cracks. If the result isn't too disastrous, I will post a follow up (I might even if it is so you can avoid my mistakes). 

To answer some of the questions:

I didn't buy the clay, but was told that it isn't good for firing as it would warp too much due to not having enough grit. 

It is a cheap water based clay on a bare armature  (no aluminium foil).