If you are getting the tone and timbre you want with the capo, I say roll with it.
That's really my main usage for capos (capoes?), to alter the timbre and response of the guitar. I rarely use it as a transposition tool only.
Especially if there is more than one guitar in the mix, you can capo one to diffrentiate the two parts sonically (Toad The Wet Sprocket does this a LOT... sorry, I NEVER have Gospel artist references... I'm a horrible forum member lol).
To me, it's a layering tool.
So, if you want to learn the song in regular tuning, go for it, it can't hurt to know it, but if you like what you get with the capo, roll with that.
Hang on, we're talking acoustic, here right? Capos aren't allowed on electrics

Oh, since wer're talking Eb, you can always just tune a 1/2 step down. The P&W team I used to play with did so many flat keys, I almost did that myself.