How To Restore A Replicated Database
If you want a standby copy of your data for HA/DR then is much better to use log shipping or database mirroring. Since these technologies create a physical database copy, you avoid exactly the problem(s) you mention. Also, schema changes 'replicate' much easier. 

If you insist on transactional replication, seed your replicas with a backup instead of a snapshot. See How to: Initialize a Transactional Subscription from a Backup for a step-by-step guide.