I voted yes, but it depends. . .
In 2nd ed I allowed an evil PC into a redominately good party. While the player who actually played the evil PC did an excellent job of not disrupting the party, the remainder of the group ended up playing witch-hunt (too much meta-gaming me thinks) and the party was so torn apart (even though none of them knew which PC was evil, in fact they were pinning it on a different PC whose player was playing extremely chaotic, but not evil, that I had to make two parties and run two separate groups/games within the same campaign. Far too mucheffort and caused a total breakdown in continuity.
Now in 3/3.5 things are much different. While 2nd ed promoted individual play (exp awards based on individual PC actions - which were often in conflict with the other PCs), 3/3.5 promotes teamwork. All exp awards (except for role-laying ones) are based on the team and split individually. This keeps the in-game backstabbing to a minimum (which far too often carries outside of the game, from my perspective). So if one player is running an evil PC and the rest are running good ones, things are fine as long as thePC work together. When they don't, well the entire party suffers but not gaining the exp they could have. A few sessions like that and the group learns quickly how to work together or they will not gain anything except the joy of "pissing" off the other PCs (and possibly the other players).
IMO it is important to lay the team concept of 3/3.5 out for the players before they create their characters and ensure they understand that unlike 2nd there are essentially no individual awards.
Personally I'm finding it harder and harder to define things in terms of good and evil within a game. Law and chaos are much easier, but good and evil tend to be a matter of the character's perspective. Maybe it's something I developed from playing Dark Sun (in 2nd ed) where good and evil was a kind of grey area - I guess that fits in with the Eberron way closer than others do.