I'm not sure that lightness of the keys would, of itself, cause problems, but there is one thing to be very careful of when it comes to electronic organ actions, and that is a certain kind of springiness. Think on this for a second: when you play a real tracker organ or even a harpsichord, you have to exert pressure on the keys in order to get past the pluck (on organs we call the spot in the keyfall where the pallets open the "pluck" because that's what it feels like) and once you've gone past that bit of resistance, it generally does not take a lot of pressure to continue to hold the keys down. The largest resistance is at the pluck.
I have, however, encountered actions (not tracker) where there is a strong springiness in the key action which causes the keys to want very badly to return while you're holding them down. This extra springiness causes the need for too much pressure to maintain the keys down during sustained notes, and I have found this to be quite problematic and uncomfortable. Even on a heavy tracker action with manuals coupled, you may need to exert a LOT of pressure to get the keys down, but not as much to keep them down. One of the worst culprits in this weird, tension causing action is FAKE tracker touch. In my experience it NEVER feels like a real tracker and is often tension inducing. If I can't have a real tracker, I want a light electric action that does not have that "springy" feeling.
But then again, there is always the possibility that the problems you're feeling do come from technique itself. I believe it's a common mistake to use too much pressure at the organ, especially among those who have learned piano first. If you are using too much pressure on the Allen, I can't see it coming from a light action (unless it's "springy" as I mentioned.) But if you are using more pressure than on another organ, I'd say it probably comes from some kind of insecurity. This often makes people hammer at the notes. Is there something else about the console that makes you uncomfortable? Could it be the pedal placement, or the bench making you feel unbalanced, or something odd about the placement of the keys?
Concerning technique itself, I did have occasional problems when I was using a technique I had been taught years ago as an "authentic" early technique. I no longer believe what that teacher told me, but the technique involved a wrist position that was in general, too low most of the time, and it caused problems. I very highly recommend a book called What Every Pianist Needs to Know about the Body by Thomas Mark. It has supplementary material about organ playing by Roberta Gary and Thomas Miles. This book involves learning about body mapping, or how we think about our body as we use it. It's very interesting information, extremely useful, and it is the book that ultimately convinced me to abandon the low wrist technique. I'm very glad I did, and very glad I read this book. I highly recommend it as a way to rethink or reconsider how you're approaching the use of your shoulders, arms, wrists, and fingers.
Beyond these suggestions, it's very difficult to make suggestions without actually seeing and hearing you play. But if you'd like to ask more about what I've written here, or ask more specific questions, I'll be happy to see if I can help.