We did "stretching" (see Janet's comment), no pushups. It certainly wasn't any closer to "conditioning" than what we do in aikido (in fact I'd say the latter is somewhat better - the wrist stretches are helpful, and we do situps). It isn't conditioning. I think the idea of conditioning is great, but I don't think the dojo is the place for it (it has a different set of goals, and it takes a lot of time), and I don't see any dojo in any style doing what I'd call conditioning.
If you rely on what you do in the dojo to create the totality of the environment which will allow you to maximize your training life, you may be missing out on many wonderful things such as nutrition, general physical preparation, quality sleep, etc..
Furthermore there are many, many budo dojo with integrated conditioning. Most Judo dojo have a warm-up that is more taxing than two hours of Aikido class, some koryu have serious conditioning built into their systems, and any dojo worth a damn needs to have a warm-up which provides for the most basic needs of its practitioners. Now there are even Aikido dojo which have classes that have a conditioning component that is either integrated into their classes or taught in separate classes. This kind of thing is pure common sense in my opinion.