Changing object scale in script while animation is running

Is it anymore possible to change transform’s scale if there’s an active animator in the object?

I have a kind of a cloud consisting of circles. Every circle object has a script attached to randomly change their scale to make the cloud seem more lively. I also have animator on the cloud to change it’s overall shape by moving the circles.

In Unity 4 this worked just fine. Animation took care of the placement of the circles and the script controlled their size. Now after upgrading to Unity 5 it stopped working. It seems that just having an animator makes it impossible to change objects’ scales by script, even if there’s no curves for the scales in the animation.

Can this kind of things be done in Unity 5 at all?

Add the object you want to animate and rescale in a empty object.
In the script you can rescale the parent object, and change the position. The scale and the position will be applied to the child.