You know what "後ろめたい" is, so let's concentrate on the first half.
「～みたいだ」 is "It seems ～" or "Looks like ～". 「持ったみたいだ」 can be translated as "It seems that I had ～".
This sentence is ambiguous by itself. Without any context given, I thought of two possible interpretations:
It seems that I made a different secret also with her.
The boy shared a secret with someone else before this. Now he (unintentionally) created another secret with this girl, too. (Yes it's something about triangle relationship.)
- あの子と = with that person (girl)
- も = also
It seems that I made a secret that is even different from her secret.
- Aと違うB = B which is different from A
- も = also, even
The boy knew something about the girl's secret, and was worrying about that. But now he feels sorry because he has another secret of his own.
And now that we have adequate amount of context given, I think the first interpretation is more likely here, although I don't know what "the first secret with someone else" actually is.