Great to hear he STTN. I think yes you will have some difficulty getting him back in his cot if you take him into bed with you at night. But if you are aware of this, and know that you will have to sleep train later, and feel for now you both need this sleep then that's okay
One thing you could do is get him caught up on sleep over the next week with you etc then (and given he is well) you could try going back to the cot. You will need to be tough on not bringing him in with you at 3 though if you want him to learn to StTn without you.