Not sure I understand the approach for modifying EMML at runtime - for this use-case scenario. How about the following...
EMML <input/> tags can have values passed to them at runtime as REST parameters.
For example in rssfilter.emml, following mashup input is defined
<input name="jobDescription" type="string" default="Java"/> <!-- Filter parameter -->
At runtime, values to jobDescription can be provided as REST param i.e.,
curl "http://localhost:8090/emml/rssfilter?jobDescription=Spring"
curl "http://localhost:8090/emml/rssfilter?jobDescription=Hibernate"
So, the values from WebForm can be passed as REST params to Mashup.
hth,
raj