I'm not too familiar with the Vary header and whether there is a good way to address this in the configuration. But if you want to remove everything including and after the first comma, you could use scan:
scan everything not a comma into precomma and the rest into ignore
scan [HTTP::header Vary] {%[^,]%s} precomma ignore
Update the Vary header value with the scan output
HTTP::header replace Vary $precomma
Else, getfield would allow you to do this without the intermediate variables:
Update the Vary header value with first field of the Vary header value, delimited by commas
HTTP::header replace Vary [getfield [HTTP::header Vary] "," 1]
Aaron