If you have two cdgas which are cofibrant (so built out of free cdgas and their cones via an iterated sequence of pushouts) and quasi-isomorphic then their homological invariants agree (one of the properties of cofibrant models is that any quasi-isomorphism between them admits a homotopy inverse). Vitali's example illustrates the problem in general: the minimal model for $H^* (S^2)$ is cofibrant, but $H^* (S^2)$ with trivial differential is not.
To clarify things a bit further, as Tom pointed out in the comments above, when we talk about derivations we usually have a map $A\rightarrow B$ of simplicial commutative rings (in characteristic zero we can use commutative dgas) and a $B$-module $M$. Since you didn't mention this data I assumed we were taking $A$ to be the unnamed field of characteristic zero and $B$ to be augmented over $A$ so that we could take the module $M$ to be $A$ (I think this is a common situation). Now $Der_A (B;A)$ is contravariantly functorial in $B$ as an augmented $A$ algebra and takes homotopic maps to the same map. So if I have maps of augmented $A$ algebras $B\rightarrow C\rightarrow B\rightarrow C$ such that the composite of each two maps is homotopic to the identity (such as when we have a quasi-isomorphism between two cofibrant $A$-algebras) I can apply $Der_A (-,A)$ to the sequence and obtain an isomorphism between $Der_A(B,A)$ and $Der_A(C,A)$.
You might find it helpful to read Quillen's 1970 paper: On the (co-)homology of commutative rings. These ideas are explained and generalized there.