I believe it's better to know how to punch, and choose not to.
Prior to studying aikido, I trained in TKD, reaching a rank of brown belt, and we spent a lot of time punching.
Done improperly, punching or atemi can easily injure your hand and wrist. Understandably, this would be severe impediment to an aikidoka.
Also, while aikido teaches atemi as a set up for another technique, i think that if the initial atemi works well, you stand a much better chance with the technique that follows.
So I say, get some bag gloves, learn how to punch, and keep going to aikido class.
In the right spirit, it's all good.