Its not good solution. Depends on your js file size, it can be painfull for your server. Best way is to use some uglify php script to generate new files. Original files just put to the non public folder. I.e:

/application 
/scripts 
/public
    /js/ {dynamic content / cache}
    /index.php

Inside scripts you put original files. You can clear cache manualy or by cron, using some special address and generating new js files. If you want automatic way, you can always check modify date of your scripts and generate new one if changed - slower, but still better way than generating scripts everytime