the \b modifier is your friend. It will match on word boundries, a zero-width assertion that will match the "Samn" in "Samn's" but not the "Charisma" is "Charismatic." i.e.

$def =~ s/\b$word\b/ <a href=$me\?word=$word>$entry[0]<\/a>/i;
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Gary Blackburn
Trained Killer