Q:

Why did the Xindi council reject using the bioweapon against humans? 

In Star Trek: Enterprise, the Xindi Reptilians secretly went into Earth's past to destroy humans using a bioweapon.  They did this secretly because Xindi council rejected the use of this bioweapon. 
Now, the question is: They wanted to fully eliminate humans (to save their future generations from humans).  So, what was the problem with bioweapon?  It was no different than the Xindi super-weapon, which was going to destroy Earth. 

A:

A physical weapon like the super-weapon is much more specific and reliable than a bioweapon.   There are very, very few diseases with 100% mortality, and not all of them are viral or otherwise weaponizable.   Say they had managed to create a virus with a 95% mortality rate.  They release it on Earth, where there are (I'll guess) 10 billion people at that point in time.  Assuming they completely fail to contain the spread and don't manage to find a cure, that leaves, worst case (for Humanity), 500 million people still alive.  500 million.  Plus a majority of those humans who live off-world: colonists, scientists.  shippers, etc.  All with a HUGE grudge against the Xindi.  Now, say the humans find a cure, and/or quarantine the virus successfully.  That could drop the total percent of the human population wiped out to 50, 25, 5 percent.  Potentially fewer.   Long story short, a bioweapon is not reliable. 
Furthermore, a bioweapon is dangerous.  Bacteria mutate.  A lot.  Viruses mutate more.  If the bioweapon infects 10 billion people, and in each person its proteins are transcoded who knows how many millions or billions of times, what are the chances it mutates into something that does affect the Xindi and somehow gets back to them?  They could well end up doing as much damage to themselves as to the Humans. 
On the other hand, they create a superweapon, go destroy the planet, all 10 billion humans on-world die, and they can easily hunt down the rest.  Quick and clean, no risk to them.