Yes, matfile won't help since it can't partially load a table.
Unfortunately, as you are now there is no workaround I'm aware of. You could always contact Mathworks support directly to see if they have a solution.
If the data is to be accessed more than once, then what I'd do is convert all these tables to Tall Tables, then save them with the write function. As far as I know there is no way to convert a regular mat file to one compatible with tall arrays so You'd have to take the performance hit once when you load the tables for the first time as regular table, but subsequent loads would allow you efficiently load only the data your require as you'd be using tall arrays.