IMO, you do not need to ghost the servers. Having said that, I have done it before, but that was when I was much less familiar with the process. 4.1.6 is absolutely in the sweet spot for being able to upgrade to 5.0 from. The benefit to upgrading the one only will allow you the flexibility to move users back and forth from the 4.1.6 BES that you know, to the 5.0 BES as you get comfortable. I would only try managing the BES's from the BAS (BlackBerry Administration Service) console after the upgrade.
This path doesn't preclude you from later adding a couple of machines for HA later. Depending on the number of users you have, you could even upgrade the one and when ready to go for the second, move all users to the 5.0 BES, depricate the second BES and use the box as the HA member to the 5.0 machine. You would then have a spare SRP and you would have higher avaiability.
The way you are describing will still involve you manually intervening if you have an issue and essentially doing a manual cutover.
Let me know if you want me to clarify.
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