Yes! Just remember to include the '-nodisplay' flag on the command line (and if in doubt, also include java -Djava.awt.headless=true to tell Java not to attempt to use the graphics environment)
java -Djava.awt.headless=true .. jalview.bin.Jalview -nodisplay -open ...
The latest version of Jalview should run fine on a server without a graphics environment, but some operations may fail. If you encounter problems, submit a bug report.