I used to practice Karate so I know a little about punching. I also know a little about Aikido - so I will try to give you my opinion. In Karate you would use a sand bag to practice the 'right' way to punch hoping that when the day comes and you need to punch somebody, then your body will be able to utilise this knowledge into punching with maximum effect concidering the situation.
In Aikido you could say, that we learn to utilize our body in everything we do, thereby we hope that if the situation arises we will be able to strike with maximum effect since our body will perform the right movement concidering the given sircumstances.
I believe the goal is basically the same yet the way to get there is different and it can be very difficult to follow two paths at the same time.
In conclusion: The best would be if you could get your heavy bag to dance around you in random patterns - now and then grabbing your wrist, so you could practice being aware of it being present and punching it when an opening occurs. The second best would be to practice striking the bag with your bodys full potential in an Aiki-way. What you should avoid is to practice a rigid style of striking where the strike is in focus, cause that could damage your feel for moving in 'Aikido-way'. It is quite okay to practice punching as a part of your Aikido-practice, but always keep Aikido in focus. This is of course only my opinion. I know some people posting in this forum are very keen on cross-training, so ask them as well. They might have a different view on the subject.
What ever you do - have fun