UPDATE: There is a counter-example!
The set is $[p_i] = [0.24, 0.24, 0.24, 0.28, 0.5, 0.5],$ and I considered two splits. The first one is a perfect split ($E[X-Y] = 0$) while the second one isn't. If my code has no bugs, here are the relevant values, with minima in red.
$$ \begin{matrix} \text{Split} & E[|X-Y|^2] & E[|X-Y|] & E[X-Y] \\ [0.24, 0.24, 0.24, 0.28] \text{ vs } [0.5, 0.5] & \color{red}{1.2488} &0.84330 & \color{red}{0} \\ [0.24, 0.24, 0.5] \text{ vs } [0.24, 0.28, 0.5] & 1.2504 & \color{red}{0.84003} & 0.04 \end{matrix} $$
So the perfect split ($E[X-Y] = 0$) does minimize $E[|X-Y|^2]$ as my older answer proved. However, the imperfect split actually has a lower $E[|X-Y|]$.
Speculation: It so happens that $P(X-Y=0)$ is higher for the imperfect split ($0.3476$) than for the perfect split ($0.3429$). I wonder if this has any bearing on the question. Also, I wonder if some kind of "symmetry" plays a role, although I did not bother to calculate the skews.
P.S. I found this by considering $[0.25, 0.25, 0.25, 0.25, 0.5, 0.5]$ and evaluating the two different perfect splits. As my older answer shows, both perfect splits have the same $E[|X-Y|^2]$ value. But as I hoped, they have different $E[|X-Y|]$ values. Then I simply perturb them a bit to arrive at the counter-example.
ORIGINAL: Not an answer, but too long for a comment.
I don't know how to minimize $E[|X-Y|]$, but your intuition (split the $p_i$'s as evenly as possible) actually minimizes $E[|X-Y|^2]$. Note that the two are not the same thing in general.
$E[|X-Y|^2] = E[(X-Y)^2] = E[X-Y]^2 + Var(X-Y)$
$E[X-Y] = \sum_{i \in \mathcal{X}} p_i - \sum_{j \in \mathcal{Y}} p_i,$ so $E[X-Y]^2$ is minimized when the $p_i$'s are as evenly split as possible. (Note that this is conceptually simple but computationally... NP-complete I think.)
Meanwhile, $Var(X - Y) = Var(X) + Var(Y) = Var(X+Y) = \sum_{all\ i} p_i (1-p_i) =$ constant. So this does not figure in the minimization.
In conclusion: splitting them as evenly as possible minimizes $E[|X-Y|^2]$.
Further thoughts: Since $E[|X-Y|^2] = E[|X-Y|]^2 + Var(|X-Y|),$ any counter-example would be such that the optimal (uneven) split has higher $E[|X-Y|^2]$, higher $Var(|X-Y|)$, but lower $E[|X-Y|]$, compared to the even split.
I found such a situation rather improbable (pardon the pun), but I don't have a proof either way.