OP - you have to weigh up the options.
1.) Leave him there and deal with some late payments.
You will still get them eventually, you will not have an estate agent to pay when they re-rent it for you and your house won't get damaged. While he is there, I wouldn't entertain any repairs other than essentials.
2.) You kick him out.
Assuming all goes to plan he leaves and doesn't cause damage, he also leaves with all rent paid up!
3.) He kicks up a stink and drags it through the court.
Costs you in legal fees, when he does go he causes a lot of damage to the house. He has no job / money so its more wasted money chasing him to repair anything (If you can even track him) and he hasn't paid the last 3 months rent...
Which do you think has the best outcome and likelihood?
I think at this stage you need to talk directly to the tenant, cut the estate agent out. They never tell you or the tenant the whole story. Explain that the late payments are causing you hassle with the bank. See if you can come to an amicable arrangement over payments or moving on.
Good luck!