We ran into a the same issue at Everything2, a Wikipedia-like site.
Our decision was to create entries with all diacritical marks
stripped, and then include both Velthius encoded and Romanized with
full diacritical marks (using HTML character entities for the marked
letters) at the top of the article. We settled on this despite the
obvious inaccuracy because of the difficulty of searching for terms
with diacriticals; most users of any English-language online site are
likely to be uncertain how to enter proper diacriticals, and may have
difficulty doing so because of the layout of their keyboard.
I would suggest that if you are creating keywords for a Buddhism- or
Pali- specific site that you name entries using the full diacritical
marks, and create some sort of a link so that someone searching for
the 'stripped' version of the word is directed to those entries. For
a more general-purpose site, I would suggest naming entries with no
diacritics and including the correct transliterations of the word in
the text of the article. It's a compromise, but we've found on E2
that locating entries by what users are likely to search for is more
useful than having correctly named entries that are difficult for many
users to find.