I haven't played in a long time so bare with me:
Mana Burn (Demon Hunter)
Dust+Entangling Roots+Surround/Focus Fire (KotG)
Shadow Strike will slow allowing you to attack him with units(Warden)
Build your wells in a manner that blocks your trees so melee heroes cant get in
Alternatively, put lumber Wisps in random places around the map instead of at all
at your main (risky)
Arcane Towers covering all peasants (Drains Mana)
Storm Bolt (MK)+Surround (Miltia, Footmen, Buildings)
^^His WW can run through but he won't come back out if he is weak^^
Use Water Elementals+AM Range to attack with Miltia as melee (AM)
Paladin can heal workers while they attack him
Nerubian Tower to slow (allows for easier chase damage)
Use Death Knight to heal Acolytes or nuke BM if you see a kill coming
Dreadlord can sleep/surround
Lich can slow as well
Also, kite Acolytes around mine, Switching Acos location when he switchs target, Bring in Ghouls to surround/attack while DK heals Kiting Acos.
Throw a few peons into burrow, definitely the ones he attacks
Build your initial Burrows so that they can cover your lumber and gold peons
Attack with wolves + range (FS)
Throw up wards or hex/surround (SH)
If you go BM you can just attack him as well for solid damage.
Rec: Whichever hero you are most comfortable with
In general, Kiting (running around/away) the peons he attacks will help prolong there life and inflict more damage to the BM for each worker kill.
This is just good all around and should become second habit early game.
Also, Another very strong approach is to counter-harass. Using natural base defenses (Towers, Wells to heal, miltia etc) as well as kiting, fend him off the
best you can while harassing his base (hopefully more succesfully) with your hero.This will force him to retreat or put you at a significant advantage exp and resource wise.
This is micro-intensive and should only be attempted if you are confident. Failing to succeed will put you at a significant disadvantage.