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.
Where LINK is a HtmlGenericControl. You could then do something like this:
VB.NET
lnkStyle.Attributes(\\'href\\') = \\'ie/styles.css\\'
C#
lnkStyle.Attributes[\\'href\\'] = \\'ie/styles.css\\' ;