What you can (and absolutely should) do is DNS delegation. On your main domain you delegate the _acme-challenge. subdomains with NS records to your DNS server that will do cert generation (and cert generation only). You probably want to run Bind there (since it has decent and fast remote access for changing records and other existing solutions). You can still split it with separate keys into different zones (I would suggest one key per certificate, and splitting certificates by where/how they will be used).
You don’t even need to allow remote access beyond the DNS responses if you don’t want to, and that server doesn’t have anything to do with anything else in your infrastructure.