Why not continue the analogy and set $\mathbb{E}(Y \, \mid \, A) = \mathbb{E}(Y , \mid \, 1_{A} = 1)$? In this case, you can check that $\mathbb{E}(Y \, \mid \, 1_{A} = 1) = \frac{\mathbb{E}(Y : A)}{\mathbb{P}(A)}$ so that it is consistent with the naive approach. Further, it's worth noting that $\mathbb{E}(Y \, \mid \, 1_{A})$ has the form
\begin{equation*}
\mathbb{E}(Y \, \mid \, 1_{A}) = \left\{ \begin{array}{r l} \frac{\mathbb{E}(Y : A)}{\mathbb{P}(A)}, & \text{in} \, \, A, \\
\frac{\mathbb{E}(Y : A^{c})}{\mathbb{P}(A^{c})}, & \text{in} \, \, A^{c}.
\end{array} \right.
\end{equation*}
I leave the confirmation of these identities as exercises, which are not too hard since $\sigma(1_{A}) = \{\phi, A, A^{c}, \Omega\}$.
An interesting fact that's worth mentioning here is that if $Y,X$ are two real random variables (you could also use random vectors, but I won't), if $\mu_{X}$ is the law of $X$, and if $Y$ is integrable, then
\begin{equation*}
\mathbb{E}(Y \, \mid \, X = x) = \lim_{\epsilon \to 0^{+}} \frac{\mathbb{E}(Y : X \in [x - \epsilon, x + \epsilon])}{\mathbb{P}\{X \in [x- \epsilon, x + \epsilon]\}} \quad \text{for} \, \, \mu_{X}\text{-a.e.} \, \, x \in \mathbb{R}
\end{equation*}
This follows from the Besicovitch Differentiation Theorem (cf. Chapter 5 of Sets of Finite Perimeter and Geometric Variational Problems by Maggi); I don't know an easier way to prove it in general. Replacing $Y$ by $1_{A}$ for suitable events $A$, we can also use this to compute probabilities conditioned on $\{X = x\}$.
On the topic of "conditioning on sets of measure zero," there is yet another fact worth mentioning. Let $U$ be a bounded open subset of $\mathbb{R}^{d}$ with smooth boundary, fix $x \in U$, and let $B^{x}$ be be a standard Brownian motion with $B^{x}_{0} = x$. Let $\tau_{U}$ be the first time $B^{x}$ reaches $\partial U$. It turns out that there is another process $\tilde{B}^{x}$ such that, for each $t \geq 0$, $B^{x}_{t}$ conditioned on $\{\tau_{U} \geq T\}$ converges in distribution to $\tilde{B}^{x}_{t}$ as $T \to \infty$. That is,
\begin{equation*}
\mathbb{E}(f(\tilde{B}^{x}_{t})) = \lim_{T \to \infty} \frac{\mathbb{E}(f(B_{t}^{x}) : \tau_{U} \geq T)}{\mathbb{P}(\tau_{U} \geq T)}.
\end{equation*}
Note that $\tau_{U} < \infty$ almost surely so here, as in the last paragraph, we have "(asymptotically) conditioned on a set of measure zero." I don't know if it's possible to interpret the statement "$\tilde{B}^{x}$ equals $B^{x}$ conditioned on $\tau_{U} = \infty$" in a more rigorous way. (More generally, in the theory of stochastic process, the previous construction is called a Yaglom limit.)