Cannot work with Government websites because or my Java Script

Fistly go to the Safari Preferences, Security tab, and actually make sure JavaScript is enabled as it can be disabled here. Additionally, you might want to try the Safari 3.0.2 beta as the WebKit implementation is different with this version and it does interact with some sites differently.

I have encountered the similiar problems, one thing you may consider since Internet Explorer for Macs is no longer really good option is use Firefox.

Sadly, the OP's problem may be due to insanely incompetant web developers, not a problem with Safari. Safari -- and Firefox -- both have completely acceptable Javascript implementations, and will do more or less anything that IE can do (modulo ActiveX foolishness). However, some web sites (i.e., those written by idiots) "sniff" the visitor's browser, and only let certain browsers through. Usually, you'll get a message saying "this site is optimized for Internet Explorer" or somesuch, with an admonition to come back using the target browser. This is possible because each HTTP request your browser issues contains a User Agent string identifying the browser and the OS.

Sniffing for specific browsers is an unspeakably foolish practice, given the proliferation of acceptable browsers at this point. 99.99% of the time, Safari would work fine on such sites if you could get in. So, assuming you've got your Javascript turned on already, and that the problem is that your browser isn't telling the site that you're running the right version of IE, then you need to use Firefox and download the User Agent Switcher add-in that will allow you to tell Firefox to tell sites it's something other than it is. (There may be a way to do this with Safari, but I don't know it.)

Yes, I'm telling you to tell your browser to lie. I do this frequently with some government sites that are coded to demand IE. While it IS possible to code a site that really does only work with Microsoft's browser (using IE-specific Javascript, or ActiveX controls, etc.), most of the time this isn't the case, and any modern browser will work if you can get past the sniffing. The User Agent Switcher add-in does precisely this, so when I visit, for example, the Wide Area Workflow site for the DoD, I set my Firefox to pretend to be IE under XP and all's well.

Another option is, of course, to just use Parallels or VMWare Fusion and thereby actually run IE, but the Agent Switcher is simpler. N.B. that it won't work for every supposedly IE-only site, but it will do the job most of the time.