I personally really like having a dedicated throw button because I dislike it when certain moves are automatically replaced by something else. I also come from other fighting games where throw is either a dedicated button or a combination of buttons.
However, my question is: Does the yomi counter activate on the frame that you are grabbed? Then, I can understand the discussion about the accidental yomi counters when two people are going for a throw and one hits the button late. However, if we want to minimize accidental yomi counters, I can see two different solutions (other than the current direction+throw will beat neutral throw if they activate on the same frame).
One solution (this one as my preferred solution) would be that for a period of a certain amount of frames after the character is grabbed (say 8 frames just to keep it consistent with the game-wide 8 frame input buffer), if the defending player presses a button, then it would not activate a yomi counter. In effect, there would be a period of 11 frames after the first player pressed throw (assuming the grab was on the first active frame) that the second player cannot press anything in order to yomi counter. This is roughly equivalent to Virtua Fighter's 12 frame buffer for a throw escape (you can input a throw escape up to 12 frames after the throw first connects). So, this would be more likely to catch people who were trying to throw at the same time. Additionally, it would place a lot less emphasis on trying to press direction+throw simultaneously from neutral in order to get the accidental yomi counter and still get the advantage of beating out a neutral throw.
Another solution would be to have neutral throw have longer startup frames. I dislike this solution because it would catch a lot of new players off-guard if they did not know the implications of this mechanic. I would rather the game be much more uniform with respect to the throw button.