i don't use tour operators so can't comment on them, just one thing though:
price list on lr site:
Lembeh Resort - NITROX Dive Packages
All inclusive - full board accommodations with breakfast, lunch, afternoon snack and dinner; unlimited tea, coffee, water; guided day boat dives NITROX for ALL dives; unlimited self guided house reef; round trip airport transfers, fuel surcharges, all taxes and resort service charge.
Not included - alcohol and soft drinks, massage and dive center gratuities.
7 nights / 17 dives 1,365USD dbl occupancey
from the price list on the lembeh resort site it looks like they are charging you over 1,300USD for the airfare, probably more because they probably don't pay list price for the accomodation at LR.
if that sounds reasonable to you then why not, but i would consider looking into arranging it yourself.
fwiw/paul