Those back muscles are doing a ton of work keeping you from falling forward. They don't work as much in the squat as in the deadlift, but they still do a lot of work in the squat.
The amount of work the lower back does is directly related to how far forward the body leans (at the hips; I'm assuming we're not discussing bent-back lifts). The lower back does a lot of work in a deadlift to counteract the torque the weight creates via the upper body lean. In a low-back back squat, the amount of work the lower body does is reduced somewhat because the lean and therefore the torque reduced. It's reduced even further in a high-bar squat, and in a front squat the back muscles are mostly doing isometric work in conjuction with the abs to keep your spine from collapsing.
Even if your squat form is bad and you're leaning excessively, you're probably not putting more stress on your back than in a deadlift. Unless maybe you're dive-bombing your squats and letting your lower back round a ton at the bottom.