Upperbound the order of P3-free partition of P4-free graphs
I update my reply in light of Aravind's comment. The claim in my previous answer was clearly incorrect but, in my defence, I never had a good intuition about graphs.

By adapting Aravind's argument you can show an upper bound of $O(\sqrt{n})$, as every $n$-vertex perfect graph has an independent set or a clique of size $\sqrt{n}$. It should be possible to show the tightness of the bound by reasoning on the tree-representation of the cograph. Consider for instance a complete binary tree $T$ with $N = 2^n$ vertices, and label its nodes as series/parallel in an alternating fashion. It represents a cograph $G$, and any $P_3$-free subgraph $H$ of $G$ must span a subtree of $T$ that does not contain three alternations along a root-leaf path; it should imply that this graph may have at most $O(\sqrt{N})$ vertices, but I leave the details to you.

A related question would be to look for a partition in bicluster graphs, as they are exactly the bipartite $P_4$-free graphs. Observe that this problem can be solved in polynomial time by computing the chromatic number of the graph: an arbitrary pairing between color classes then gives the optimal partition.