Depending on your licencing model/technology, the long confirmation times might not be a problem.
If your client needs an active licence that is checked often (each startup, every 24 hours, at random intervals,...) you can deliver a licence as soon as somebody broadcasted a transaction (allowing 0 confirmations). If the transaction isn't confirmed after 24 hours, or if the inputs get double spent, you can just withdraw your licence, so the person trying to scam you just had a free demo, but was kicked out before he had practical use for your software.
If it's a web-based service, it's even simpler... Just lock their account if the transaction isn't confirmed after 24 hours, no worries

It would be a whole different thing if you were selling physical goods... Once they are sent, it's pretty hard to get them back if the transaction doesn't confirm, or if the sender double-spends. Same thing goes for a lot of digital downloads that don't require a licence, but in your case, i don't see a problem.