If you indeed have based and have freebase harmalas, there won't be NaCl salt contamination. The NaCl from the previous step wouldn't be there because you redissolve the harmalas HCl from manske in water, which will also dissolve any excess NaCl. Then when you add NaOH or Na2CO3 to the harmala solution to precipitate the freebase, it will precipitate harmalas but not the dissolved NaCl.
The possible contamination would only be excess Na2CO3 or NaOH if you added the base directly to the harmala solution and didn't mix well and some stayed undissolved on the bottom. If you first make a concentrated solution with the base and then add that to the dissolved harmalas solution, you completely eliminate that possibility.
If you screwed up and you did have some undissolved base there, you could do a quick dilute basic water wash on the harmalas but you can lose a small bit of harmaline with each wash because harmaline freebase is slightly soluble in water .
If what you have is not a base but the result of a manske precipitation (harmalas HCl), then obviously you can't wash it with water because it will simply dissolve it.