Hey Gillian,
I haven't mixed the RSiteCatalyst package with Alteryx, but I have automated RSitecatalyst Reporting by creating a batch file that calls my RSiteCatalyst script and scheduling it to run automatically in the Windows Task Scheduler. It was a couple of years ago, but I believe there was an issue where the RCurl package that RSiteCatalyst uses needed to be explicitly called when used in batch mode, so I'd check just changing your script to make that explicit call and see if it then works in Alteryx.
If not, you can automate your RSiteCatalyst Script produce a csv and then pick that up with Alteryx. The second answer on this thread (http://bit.ly/1OxGOVq) shows how to run R from command line/batch. You can then automate your batch file in Windows using these directions (http://bit.ly/1LPR5Wg). If you have a different OS, simply google "How to schedule a batch file to run automatically in my OS".
I hope this helps. Thanks!