You can run both on the same site, but won't be able to talk to each other unless you setup some sort of messaging system or share storage.They are basically applications of complete different nature.
Another possibility is to call your .NET code from PHP:
A piece of code written in C# like this:
string javascript = "";
Microsoft.Ajax.Utilities.Minifier m = new Microsoft.Ajax.Utilities.Minifier();
Microsoft.Ajax.Utilities.CodeSettings settings = new Microsoft.Ajax.Utilities.CodeSettings();
settings.OutputMode = Microsoft.Ajax.Utilities.OutputMode.SingleLine;
settings.PreserveFunctionNames = false;
string minified = m.MinifyJavaScript(javascript, settings);
Will look like this on PHP:
$minifier = netMinifier::Minifier_Constructor();
$settings = netCodeSettings::CodeSettings_Constructor();
$csssettings = \ms\Microsoft\Ajax\Utilities\netCssSettings::CssSettings_Constructor();
$settings->OutputMode(\ms\Microsoft\Ajax\Utilities\netOutputMode::SingleLine());
$settings->PreserveFunctionNames(FALSE);
$settings->QuoteObjectLiteralProperties(TRUE);
$result = $minifier->MinifyStyleSheet($css, $csssettings, $settings)->Val();
From:
http://www.drupalonwindows.com/en/blog/calling-net-framework-and-net-assemblies-php