import re
words = ["apple", "orange", "plum"]
s = 'Sita has apple and "plum" and loves drinking snapple'
print(re.sub(r'\b(?!<")(%s)(?!")\b' % '|'.join(words), r'"\1"', s))
aW1wb3J0IHJlCndvcmRzID0gWyJhcHBsZSIsICJvcmFuZ2UiLCAicGx1bSJdCnMgPSAnU2l0YSBoYXMgYXBwbGUgYW5kICJwbHVtIiBhbmQgbG92ZXMgZHJpbmtpbmcgc25hcHBsZScKcHJpbnQocmUuc3ViKHInXGIoPyE8IikoJXMpKD8hIilcYicgJSAnfCcuam9pbih3b3JkcyksIHInIlwxIicsIHMpKQ==