I know exactly what you mean, and unfortunately there isn't much to do for it now. You can add some butter to try and divert your taste buds LOL but it won't change the rawness of the roux.
When making a roux for chowder cook it until it's a pale yellow/golden color. You definitely don't want it to darken as you would for jambalaya, but it does need to cook for several minutes.
The other option is to make a chowder without using a roux. Those recipes are quite nice too.