You can examine the Request.UserAgent to check if the browser was IE, define a custom HtmlGenericControl type representing your stylesheet link and set the href property on it depending on if the browser was IE.
<LINK rel=stylesheet runat='server' id='lnkStyle'>
Where LINK is a HtmlGenericControl. You could then do something like this:
lnkStyle.Attributes('href') = 'ie/styles.css'
lnkStyle.Attributes['href'] = 'ie/styles.css' ;