SafariDriver alert handling possible workaround using HTTP requests & responses. This may or may not work for you depending on what your application under test does with the alerts.

SafariDriverAlertWorkaroundExample.java

 /* Safari workaround below simply constructs the required HTTP POST data
  * as key/value pairs (e.g. param1=value1&param2=value2, etc.)
  * then makes an HTTP POST request with that data, then check the received
  * HTTP response returned (e.g. status code 200 OK, or response body content contains what you expect)
  * Example below currently skips checking response as that part is handled by the CustomHttpClient
  * (implementation not shown). Making actual HTTP POST request is same thing. For details on that,
  * see this for reference:
  * http://stackoverflow.com/questions/2793150/how-to-use-java-net-urlconnection-to-fire-and-handle-http-requests
  * http://stackoverflow.com/questions/9129766/urlconnection-is-not-allowing-me-to-access-data-on-http-errors-404-500-etc
  *
  * You'll have to spy on what your web application does when alert is accepted to see if you can do something similar.
  * Spy using HttpFox, LiveHttpHeaders, ieHttpHeaders, Firebug & similar browser developer tools to profile network
  * requests, or Wireshark, etc.
  */
 public void removeItemsFromCart(String currentSite) throws Exception {      
    	if (browser.browserName != BrowserName.SF)  { //for non Safari browsers
        ArrayList<WebElement> itemsInCart = (ArrayList<WebElement>) driver.findElements(By.xpath(REMOVE_ITEM_LNK));
    		int nItem = itemsInCart.size();
    		for (int i=0; i<nItem; i++) {
        		itemsInCart.get(i).click();            
            Alert alert = driver.switchTo().alert();
            //String AlertText = alert.getText(); //return this if you needed it...
            alert.accept();
        		Thread.sleep(1000);
        		driver.navigate().refresh();
        	}
    	}
    	else{ //Safari workaround: Cannot handle confirmation    		
    		String url = currentSite;
       	//setup objects for removing cart items
    		ArrayList<WebElement> cartItems = (ArrayList<WebElement>) driver.findElements(By.xpath(REMOVE_ITEM_LNK));
    		CustomHttpClient httpClient = new CustomHttpClient();
    		httpClient.cookies.put("PHPSESSID", driver.manage().getCookieNamed("PHPSESSID").getValue());
    		httpClient.queryParams.put("method","removeItem");
        
    		//for each cart item "ID", make HTTP POST to web server for removing cart item 
        //(to mimic what browser client side code would do after accepting alert)
    		for (int i = 0; i < cartItems.size(); i++) {
    			//note that a put() will overwrite previous value, so no need to remove beforehand
    			httpClient.queryParams.put("cartItemId",cartItems.get(i).getAttribute("id"));        		
        	httpClient.postFormData(url + "/cartItemRemovalApiPath");
        	//for test optimization, we refresh page after removing all items (externally)
    		}
    		driver.navigate().refresh();
        }
    	if(!isTextPresent("Your shopping cart is empty")){
    		throw new Exception("Cart item removal failed, cart not empty.");
    	}
    }