I hope it's okay to post an answer to my own question. I am essentially repeating Woodin's proof that he just showed me. Any errors were probably introduced by me.
Recall that under AD all measures on ordinals are countably complete and ordinal-definable.
By the coding of measures theorem of Kechris assuming AD and that there is a Suslin cardinal above $\kappa$, there are fewer than $\Theta$ many measures on $\kappa$ (or $\kappa^{<\omega}$ for that matter.)
So we may push forward Martin's measure on $\mathcal{P}_{\omega_1}(\mathbb{R})$ to get a fine, countably complete measure $U$ on $\mathcal{P}_{\omega_1}(\operatorname{meas}(\kappa^{<\omega}))$, where $\operatorname{meas}(\kappa^{<\omega})$ is the set of all measures on $\kappa^{<\omega}$.
Fix a tree $T$ on $\omega\times \kappa$. As usual, given a real $x \in \omega^\omega$ we let $T_x = \lbrace s \in \kappa^{<\omega} : (x \restriction |s|, s) \in T\rbrace$.
Claim: $U$-almost all $\sigma$ witness the weak homogeneity of $T$.
Proof: For each $\sigma$ we define a game $G_{\sigma}$, closed for Player I, for which Player I has a winning strategy iff $\sigma$ does not witness the weak homogeneity of $T$.
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I plays: $(x_0, \alpha_0, \beta_0)$, $(x_1, \alpha_1,\beta_1),\ldots$
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II plays: $\mu_0$, $\mu_1,\ldots$
Let $x$, $\vec{\alpha}$, $\vec{\beta}$, and $\vec{\mu}$ denote the resulting sequence of moves.
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Rules for I: $\vec{\alpha} \in [T_x]$ and the sequence $\vec{\beta} \in \mathrm{Ord}^\omega$ continuously witnesses that the tower $\vec{\mu}$ is illfounded.
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Rules for II: $\vec{\mu}$ is a tower of measures in $\sigma$ concentrating on $T_x$.
If both players follow the rules until the end, we say that player I wins.
If $\sigma$ does not witness that $T$ is weakly homogeneous, say $x \in p[T]$ but there is no wellfounded tower of measures in $\sigma$ concentrating on $T_x$, then there is a continuous witness to the illfoundedness of towers of measures in $\sigma$ concentrating on $T_x$. (This is proved by an argument similar to what follows but using a fine, countably complete measure on the set of subsets of $\kappa^{<\omega}$.)
So if $\sigma$ does not witness that $T$ is weakly homogeneous, then player I has a winning strategy in $G_\sigma$. (The $x$ and $\vec{\alpha}$ are fixed in advance and the $\vec{\beta}$ comes from $\vec{\mu}$ via the continuous witness mentioned above.) Assume toward a contradiction that for $U$-almost every $\sigma$, player I has a winning strategy in $G_\sigma$. The game is closed, the moves are ordinals and measures, and all measures are ordinal-definable, so for such $\sigma$ player I has a winning strategy $F(\sigma)$ of playing the least move leading to a subgame where he or she still has a winning strategy.
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Define the integer $x_0$ to be the one played by $F(\sigma)$ on the first turn for $U$-almost every $\sigma$.
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Define a measure $\mu_0$ on $\kappa$ by $A \in \mu_0 \iff \forall^*_U \sigma\; (\alpha^{\sigma}_0 \in A)$ where $\alpha^{\sigma}_0$ is the ordinal $\alpha_0$ played by $F(\sigma)$ on the first turn.
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Define the integer $x_1$ to be the one played by $F(\sigma)$ on the second turn against $\mu_0$ for $U$-almost every $\sigma$.
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Define a measure $\mu_1$ on $\kappa^2$ by $A \in \mu_1 \iff \forall^*_U \sigma\; ((\alpha^{\sigma}_0,\alpha^{\sigma}_1) \in A)$ where $\alpha^{\sigma}_1$ is the ordinal $\alpha_1$ played by $F(\sigma)$ against $\mu_0$ on the second turn.
Continuing in this way, we get a real $x \in \omega^\omega$ and a sequence of measures $\vec{\mu}$. One can easily check that $\vec{\mu}$ is a tower of measures.
Each $\mu_i$ concentrates on $T_x$ because $(\alpha_0^\sigma,\ldots,\alpha_i^\sigma) \in T_x$.
It is a wellfounded tower because if $A_i \in \mu_i$ for all $i<\omega$ then by countable completeness of $U$ there is a $\sigma$ such that $(\alpha_0^\sigma,\ldots,\alpha_i^\sigma) \in A_i$ for all $i<\omega$.
However, by countable completeness of $U$ there is a $\sigma$ such that $\vec{\mu}$ is a legal play by player II against player I's winning strategy $F(\sigma)$, so player I's moves $\beta^\sigma_i$ continuously witness the illfoundedness of $\vec{\mu}$. Contradiction.