I have not read the full article but permit some observations.
The arguments raised here are similar to one raised by similiar organisation in Australia. While their policies sound nice and warm and fuzzy they are down on practicalities.
The article seems to suggest that 'native' species of bees can do the job of pollinating better that the honey bee. If such were the case, one would have to ask why then is there such a problem with pollination? The answer is simply that 'native' species are not up to the task. If 'native' species were the answer beekeepers would have switched from honeybees to 'natives' a long time ago.
Similar arguments are used in Australia. We have some 'native' bee species and while they might be good at pollinating the eucalypt forests they are just not us to the job of commercial pollination - and they are hard to manage. However, these groups do have a strong political lobby front and are popular with the urban elite so they do attract bucket loads of $$$$. In some States apiarists have been locked out of state forests and national parks but apparently no one has told the bees who failed to understand imaginary lines drawn on imaginary maps.
The end result of this so-called 'debate' is that without honeybees the population would starve. A somewhat similiar argument is uses in Australia to try stop beef production and arguing for the 'production' of kangeroo meat. If kangeroos where all that great farmers would have switched two hundred years ago.
As many Australia graziers and farmers are finding out, setting aside land for the 'natives' does not pay the bank mortgage or the fuel bills or the land taxes - which are rising at a faster rate than the 'natives' can 'regenerate' the land. And, I have a problem with urban elite 'immigrating' to the country with their forty or hundred acre plots with their warm and fuzzy ideas and thereby render yet more land unavialable for food production. Like 'peak oil' their is 'peak land' - the point at which the cost of farming marginalised land will fall to the point of being unviable.
An increasing world population demands and ever increasing production of food from a diminishing suppy of arable land. We can't have it both ways.
Sorry. Time to get off the soapbox.
Native bees are certainly up to the task and because there's 4000 native species, when one doesn't do very well one year others will fill in the gap. The trouble is pesticides do a great job of killing them. Even in safer forms if a mason or digger bee were to bring back poison coated pollen to the burrow she's just killed off her life's work. Leaf cutter bees too, when they take back contaminated leaves.
Even when they aren't contaminated, nests can still be destroyed by fire. Plowing a field will kill off all developing digger bees that might be in the soil, those below the plow won't have a way out of the burrow. Because they're only active for 4 to 6 weeks of the year you really have to look at it in terms of generations. One of these bees can make one or more nests that account to 20 to 30 developing bees. It could be worth it to a farmer to simply set aside a patch of dirt, Undisturbed, and at least 25 feet away form the spraying zone. Nesting blocks are certainly worth your time.
Solitary bees aren't distracted by the best food source around they're only interested in providing their young with food. And they rarely forage more then a half mile from their nest.
Native bees come in a variety of sizes! Have you ever seen a honey bee try to fit it's head in a blueberry flower? They don't bother, they wait for another bee to chop a hole up in the side and they just steal the nectar. Some are specialized in a particular crop. The Blueberry bee for example, (like a really tiny bumblebee) or Squash Bees. The male Squash Bee actually spends the night inside the Squash flower.
These little guys offer 100% seed production.
These farmers who are doing the native pollination thing are only spraying insecticide 4 times a year or when needed. As opposed to the other farms who look at their calender and spray on the date 6 times or more regardless of there being a problem. I don't know how much it costs to spray a field but think of the money they're saving. "Only spraying when there is a problem worth spraying," gasp.
Also, honey bees tend to only forage for either nectar or pollen on a single trip. This means if a plant has two different sexes of flowers, honey bees won't likely result in pollination. It's like half the bees are doing nothing.