Well, I think there are definitely going to be some disadvantages. But it depends on what you want to play.
By the way, do I assume correct you want to play at the same tone height as normal style?
If all you want to play is chords, there shouldn't be too much problems. You don't lose chords, you just have to play them differently. For example the E,F and G chords you name, you would just have to play like the B, C and D are played normally. Basically what you would have to do for every chord is look at this:
Take the chord you want to play, and go 5 steps (half tones) down or 7 up (which is the same). And then play it that way with the capo at 5th fret.
One annoying thing with this of course would be, if you want to learn something from someone else by looking at how he plays it, you have to do everything different.
Of course if you want to play more complex things, like classical music pieces, at the same tone height but at the 5th fret, that will become almost impossible. You don't have the low basses, and the fingering will be difficult/impossible, because it has been written for normal position. You can of course play them, but at higher tone. For a lot of pieces, this won't be a problem. But your range is smaller, which can be a problem for some pieces.
Actually I would also suggest you to buy a smaller guitar, and maybe some softer strings. Then everything stays the same as for a normal guitar. But if a smaller guitar is still painful, a capo in the 5th is a good solution. There will be some disadvantages, but a lot can be overcome in some way.