You actually already have the result: one can always define an operator
$$\hat{\pi}_{ml}\equiv (\mathbb{I}_s\otimes \langle A|_a) \hat{U}^\dagger_{sa} (|m\rangle_s\otimes |l\rangle_a)(_a\langle l|\otimes \vphantom{a}_s\langle m|)\hat{U}_{sa}(|A\rangle_a\otimes \mathbb{I}_s),$$ where I just added some parentheses, added a subscript $s$ for the system Hilbert space, added the subscript $sa$ to the unitary because it acts on both, and added identity operations for the system. We simply match the parts for each subspace to obtain
$$\hat{\pi}_{ml}=\mathbb{I}_s (\vphantom{a}_a\langle l|\hat{U}_{sa}|A\rangle_a)^\dagger |m\rangle_s \vphantom{a}_s\langle m|(\vphantom{a}_a\langle l|\hat{U}_{sa}|A\rangle_a) \mathbb{I}_s=(\vphantom{a}_a\langle l|\hat{U}_{sa}|A\rangle_a)^\dagger |m\rangle_s \vphantom{a}_s\langle m|(\vphantom{a}_a\langle l|\hat{U}_{sa}|A\rangle_a) .$$ The operator in parentheses $(\vphantom{a}_a\langle l|\hat{U}_{sa}|A\rangle_a)$ is just an operator on the system.
As to the properties of $\hat{\pi}_{ml}$, one would have to prove more things, but that is not the focus of this question.
Why did we define it like this? We simply expanded the absolute square $|\langle a|B|c\rangle|^2=\langle a|B|c\rangle\langle c|B^\dagger|a\rangle=\langle c|B^\dagger|a\rangle\langle a|B|c\rangle$ to find
$$\left|(_a\langle l|\otimes \vphantom{a}_s\langle m|)\hat{U}_{sa}(|A\rangle_a\otimes |\psi\rangle_s)\right|^2=(\langle\psi|_s\otimes \langle A|_a) \hat{U}^\dagger_{sa} (|m\rangle_s\otimes |l\rangle_a)(_a\langle l|\otimes \vphantom{a}_s\langle m|)\hat{U}_{sa}(|A\rangle_a\otimes |\psi\rangle_s).$$
Now, your main confusion probably comes from not being used to operators that act on two systems. So let's just be clear and say that any such operator can be decomposed as
$$\hat{M}_{sa}=\sum_{ijkl}m_{ijkl}|i\rangle_s \vphantom{a}_s\langle j|\otimes |k\rangle_a\vphantom{a}_a\langle l|.$$ Making this operator unitary, or choosing whether it entangles two systems or not, depends on the coefficients $m_{ijkl}$, but such a decomposition always exists. This lets us compute things like, for
$$\hat{U}_{sa}\equiv\sum_{ijkl}u_{ijkl}|i\rangle_s \vphantom{a}_s\langle j|\otimes |k\rangle_a\vphantom{a}_a\langle l|,$$
$$\vphantom{a}_a\langle l^\prime|\hat{U}_{sa}|A\rangle_a=\sum_{ijkl}u_{ijkl}|i\rangle_s \vphantom{a}_s\langle j| (\vphantom{a}_a\langle l^\prime|k\rangle_a\vphantom{a}_a\langle l|A\rangle_a).$$ This is just a new operator
$$\hat{M}_s=\sum_{ij}m_{ij}|i\rangle_s\vphantom{a}_s\langle j|$$ acting on the system alone, with coefficients that depend on $l^\prime$ and $A$:
$$m_{ij}=\sum_{kl}u_{ijkl} (\vphantom{a}_a\langle l^\prime|k\rangle_a\vphantom{a}_a\langle l|A\rangle_a).$$