You can work around this by storing the currently focused element before calling autoSize()
and then using the OnClientAutoSizeEnd event (http://www.telerik.com/help/aspnet-ajax/window-client-side-events-onclientautosizeend.html) to restore the focus.

//this goes in the content
function autoSizeWnd() {
	//code that manipulates the content so autosizing is needed
	var oWnd = getRadWindow();
	if ($telerik.isIE) { //assumes you have the Telerik core client-side libraries loaded (e.g., by having a Telerik control on this page). If you don't, you can skip the check or add them manually
		oWnd.__currActElem = document.activeElement;
	}
	oWnd.autoSize();
}


//this goes in the main page where the RadWindow is declared
function autoSizeEndHandler(sender, args) {
	setTimeout(function () {
		if (sender.__currActElem && sender.__currActElem.focus) {
			sender.__currActElem.focus();
		}
	}, 0);
}