While you're correct that you'd need javascript to do this, this isn't really an Illustrator Scripting question. This is a web development question. You'd need to generate your SVG in illustrator (or similar vector editing program) but the mouseover effects you're talking about require linked or embedded javascript within the code for the website.
This particular forum is for coding/automating the inner workings of illustrator with javascript (or applescript or VBS). For example, renaming different layers, paths or groups inside an illustrator document.
That said, if you said you could write the code to create hyperlinks for each section of the map, you can write the code to change colors with mouseover. You simply need to target the element, add an eventListener for mouseover, then set the resulting function to update the CSS property for the targeted element. You'll also want to add a "mouseout" or "mouseleave" event listener to set the color back to the default whenever the mouse moves away from the target element.
Good luck. =)