I don't think your problem is an imageJ problem. You need to read more about using Java programs through browsers.
I haven't done very much with deploying Java applets, so I'm just going to refer you to some websites that I would be reading if I were in your shoes.
Describes the many different ways to use Java through browsers:
http://mindprod.com/jgloss/signedapplets.html#JWSExample of a signed applet:
http://bij.isi.uu.nl/applet.htmA tutorial on how to use Java Web Start:
http://download.oracle.com/javase/1.5.0/docs/guide/javaws/developersguide/development.html#introA few demos using signed/unsigned applets and java web start to deploy imageJ:
http://rsb.info.nih.gov/ij/applets.htmlGood luck!