Direct web interface for Malayalam input

I had attempted this here:
http://varamozhi.sourceforge.net/sallaapam/index.php

There I used PHP and varamozhi executable for kerala font. This
executable is available in C:\Program Files\Varamozhi Editor\bin
directory. When preview is pressed, varamozhi executable is given the
text as input and output is displayed back.

You could also take different route also: Varamozhi can provide a
linkable C library which has an interface function to which you pass
manglish and get back the string in a specific font.

Which font are you trying to use in the site? You could allow smooth
transition from conventional fonts to Unicode by keeping the text in
manglish internally and displaying it with respect to a user
configurable(cookie) which stores desired font for that particular
user. Essentially user desides in which font(including unicode) he
would likes to see the malayalam text.