There's a lot of misinformation in this thread.
Firstly, the yellow unsupported device banner at the top of Google Wallet means nothing. You'll still be able to use Google Wallet. Only rooted users will see it. It's basically warning you that if you mess up, Google aren't liable.
Secondly, there are two types of secure element errors that you'll get. If you get an error saying that there are insufficient secure element privileges, this is to do with your custom ROM being crap. This error is fixable, as it's merely to do with incorrect permissions in the ROM. Using wlpywd's linked workaround could work.
The second secure element error reads as 'secure element not responding' or 'secure element not found'. This is the error that results from not clearing Wallet prior to flashing. If you get this error, there is absolutely nothing you can do other than getting a new phone. Changing build prop or anything else will have no effect - the secure element hardware is now corrupt. Restoring backups will have no effect.
Some have suggested that custom ROM developers could include Wallet wiping as part of the flashing process. This is impossible. When you wipe Wallet, you're wiping the secure element. Only Google has the ability to gain access to the secure element through software. That's why it's secure. It's impossible for ROM developers to gain access to and wipe the secure element without begging Google for the keys.
---------- Post added at 07:34 PM ---------- Previous post was at 07:30 PM ----------
You'll still be able to use NFC for Android beam and to scan NFC tags. The destruction of the secure element means that you'll be unable to use other NFC financial services in the future. It also means that if Google ever allows card emulation on Android in the future, you won't be able to use it for access control and ticketing.
However, there is still some hope. Phones can have multiple NFC secure elements. Rumour has it that ISIS will be using the SIM card as the secure element. If this is the case, people with messed up embedded secure elements will still be able to pay for goods with their phones via the SIM secure element.
Sent from my Epic Touch (Blazer ROM) using XDA