Most likely, unless your players are in the very corner cases of the system, it probably doesn't matter which system you use and switching shouldn't be an issue.
The big differences are that your player won't just be able to buy anything they want anymore (uncommon and rare items can only be found, not usually purchased...at least not easily).
The other thing is that sale prices change based on rarity.
Again, unless your players have significant combinations that are game breaking, you shouldn't have any trouble switching. And around L6 they're probably looking to swap or upgrade most of their current stuff anyways.
The one thing you might do is make a list of all the items they have right now and compare it to the item rarity lists vs what they should have. This will tell you if there is any great imbalance you might want to correct as you go forward.
The important thing here is that this is something your players want, and it's not something to keep from them IMO. That said, make sure you guys keep open lines of communications and that they know if you spot something game breaking going on, that you might ask them to rework their gear.
Two other considerations that should be mentioned:
Upgrading items becomes far more important. If I can't just buy what I want, using (or finding a wizard to use) Enchant Magic Item, to upgrade the weapon/implement/armor/neck item I use for my attacks is more important (especially if you're using frost cheese or radiant mafia come paragon where the enchantment of your item makes your build tick)
Use wishlists. 4e treasure load out is predicated on the PCs getting stuff they want and will use. If they are selling current level items, something is wrong. Make sure you give them the stuff they need/want.