Can I exclude a portion of the building?

"Can I exclude the warehouse from consideration for this credit?" - No

You may want to keep a look out for the Warehouse "adaptation" coming soon. I believe it addresses this issue.

What is the Warehouse "adaptation"? Is this going to be part of ASHRAE Standard 55 or a LEED ruling? Where would we look for this?

Is it a High Bay warehouse ?

The LEED Adaptations are basically versions of LEED for specific building types. Think "LEED for Warehouses"

Is there an update on the status of alternative compliance for warehouses? Controllability of systems and thermal comfort have both been very hard to achieve in all of our large mixed-use spaces like this. I am working with a client in food and beverage on a large manufacturing and high-bay warehouse base, with a multi-story office in the plant. All spaces will comply with at least the minimum 30% over ASHRAE 62.1, offices will comply with ASHRAE 55, but the energy required to condition the warehouse and production space would make this not be advisable. The mechanical ventilation in the warehouse and production area is zoned, based upon occupancy, and the dual-speed fans are controllable VIA a hand switch or by the BMS. I have read the CIR:

http://www.usgbc.org/LEED/Credit/CIRDetails.aspx?RequirementID=709

And even though they had a similar problem, GBCI really sidestepped the issue as it assumed natural ventilation, which in food processing is not an option due to strict pest control.

In our opinion, the dual speed fan would comply with the intent to provide increased thermal comfort, but it is a hot/humid climate near the equator, so without conditioning, we would never get in the right range of comfort for ASHRAE 55. Any input?

You should take a look at the current public comment versions for the next (2012) LEED Update (available at USGBC.org). They include draft language for all the proposed adaptations (Warehouse, Hospitality, Data Centers). You might want to try to use the draft 2012 language as an alternative compliance path.