You are basically right about salt and yeast not being entirely compatible. Because of this, bakers have come up with possible solutions. One solution that has been recommended (by Neapolitan pizza experts, among others) is to combine the salt and yeast with equal amounts of water in separate containers, and, similarly, divide the flour for the dough in two and put into separate containers (for a total of four containers). The salt-water mixture is then combined and kneaded with the flour from one of the flour containers, the yeast-water mixture is combined and kneaded with the flour from the other flour container, and the two separate doughs are brought together in a final step and kneaded into a single dough ball.
An alternative approach, one that I almost always use--no matter what a recipe says to do--is to mix and knead all of the dough ingredients except for the salt and, toward the end of the kneading process, add the salt called for in the recipe and knead a bit longer until the salt is fully incorporated. This is a technique borrowed from professional bread makers. What is important is not to forget to add the salt, which is easy to do in the haste to move on to the next step.
The above applies principally to the use of wet yeasts and dry yeasts other than instant yeast. Randy and others are correct in that it is OK to combine instant yeast with the other dry dough ingredients, including salt. Apparently the instant yeast is more tolerant of salt than the other forms of yeast. I have tried both approaches when using instant yeast--adding the salt last and mixing the salt with all the other dry ingredients at the beginning (usually flour, instant yeast, and sugar), and have not detected any difference in the two approaches. From what I have read at PMQ, based on tests they have done, all of the standard forms of wet and dry yeasts operate in much the same way from the standpoint of chemisty, so there should be no noticeable differences (e.g., in fermentation or taste of the final baked crust) from using the different yeast forms. The main difference between the various types of yeast is basically availability, convenience of use, and perishability. I have gone entirely to instant yeast as a result of what I have read on yeast and my own personal experiences. Of course, there will always be some who will prefer one form of yeast over another based on their palates and experiences.