IMO, one of the most important things when evaluating any new product/service (free or not) is to gauge the overall impact on your workflow. Will this be more productive? Will things be easier overall? What may save you more time in one area, may cost you more in another. It's up to you to decide what you can live with (or without.)
In the web dev community, (S)FTP/SSH is essentially commonplace. No SFTP/SSH would be a deal breaker for me, but at least there are paid options supporting this requirement.
I am glad I was able to experience MODX Cloud during the free beta period when (S)FTP/SSH was available. Unfortunately, lack of database tunneling and other command line tools helped me realize how important certain pieces of my workflow were, no matter how enticing MODX Cloud still is. It's unfortunate that the free Lab Plan isn't an apples-to-apples comparison with the paid plans. Will I still use one on occasion? Probably.
I could see this leaving many non-paying users ultimately wanting
more, which is most likely good business. I am curious to see what other features in the 2013/2014 Cloud roadmap will remain exclusive to paying customers. In the end, my excitement regarding the recent Lab Plan announcement was knocked down a few notches today.