@David_Morrow,
In my experience, it is always better to read the file into JMP and perform filtering out of columns or rows after the data is in a JMP data table. This would be especially true when the data you want to exclude is not in a squential order. Most programming languages have optimized csv/xlsx readers built in. Unless you are willing to re-shape your table in such a way that , you can move all the columns to be filtered to one end and read the columns on the other side, I don't think filtering out alternate columns might be really helpful in this case.
Additionally, when you are opening the .csv file using the Open() are you making it a private data table ? Making a data table private while opening a file makes it a lot faster.
Best
Uday