The problem with Route 53 is that it doesn't play with other DNS servers. It is a completely self contained solution. This means that if you used Route 53 your internal servers could only look up through the VNet into Route 53, you couldn't have a secondary Nameserver onsite that took a zone transfer from Route 53 (they don't support them)
You could potentially have caching nameservers internally, and have long expirely times on your host records, so if there was any problem the records wouldn't go stale but this brings its own set of problems.
This leaves you with a couple of solutions.
Use your internal network entirely, set up your internal name servers, internal.example.com and have a secondary name server located inside your Vnet that AWS clients can refer to. This way if there is a problem with the link, both sides still have working DNS.
Alternatively, you could configure internal.example.com in the same way, but then have aws.example.com running on Route 53. (or on a standalone server)
If Route 53 supported Zone Transfers and secondary servers it would be largely irrelevant what you went with but because they don't any solution you build is going to mean rolling some sort of glue to sit in between everything. This is invariably a Very Bad Thing™