volvie, that letter was meant for a yeshiva that had only been using cholov yisrael milk for years, and was thinking of switching to cholov stam. R’ Moshe’s letter to them said only b’shas hadchak. That is clearly not the everyday case that applies to everyone. Additionally, it’s been said by many poskim in E”Y now that a psak should only be followed by the general public when it’s written down as a teshuva, and a psak directed at a specific person or group applies only to that person/group. Therefore, R’ Moshe’s letter does not apply to the general public, it only applied to that yeshiva.
The OU also has an article about this. R’ Belsky gives a psak that allows cholov stam for a different reason than R’ Moshe did. You can read it on the OU website: http://www.oukosher.org/index.php/common/article/1377721