For some reason your link isn't working for me. Here's a link that discusses the checks and blances within governments:
http://en.wikipedia.org/wiki/Checks_and_balances
In this link you'll notice the Executive Branch of the Federal Government has:
Police powers of arrest, detainment, and search This is why federal law enforcement officers are under the EB.
What you'll also find on this site is:
The American states mirror the executive/legislative/judicial split of the federal government. Major cities tend to do so as well, but in general, the arrangements for local and regional governments vary widely. Because the judicial branch is often a part of a state or county government, the geographic jurisdiction of local judges is often not coterminous with municipal boundaries.
In many American states and local governments, executive authority and law enforcement authority are separated by allowing citizens to directly elect public prosecutors (district attorneys and state attorneys-general). In some states, judges are also directly elected.
Many localities also separate special powers from their executive and legislative branches, through the direct election of police chiefs, school boards, transit agency boards, park commissioners, insurance commissioners, and the like.
I think what you're confusing is the difference between federal law enforcement and state and local. The Federal Government does not control local law enforcement. They often work together, but not always. Consider the current situation with medical marijuana laws. Here in Oregon state and local LE will not arrest or prosecute individuals for the possession or manufacture of marijuana if they have a state issued card. Federal LE will arrest and prosecute regardless of the individuals status with the State.
This issue has gone as far as the Supreme Court. The Supreme Court's 2005 decision did not expand the powers of federal law enforcement agencies like the DEA; it only affirmed that they can enforce federal laws prohibiting the use of controlled substances, regardless of state, county, or municipal law. It is not anticipated that federal agents will step up efforts against state-authorized growers, dispensaries, or patients because of this decision. State and local law enforcement officers, who are responsible for the enforcement of state and municipal laws, will most likely continue to honor the democratic decisions that their residents have made about marijuana policy.
If, as you seem to think, LE in this country was under the EB there would be no reason to have these cases. The EB would simply tell local LE to enforce these laws. But that's not the way it works. Here in Oregon right after the SC ruling the Attorney General for the State directed the State to temporally stop issuing cards. Within weeks he issued an opinion stating the State of Oregon's voter's wishes can not be over ruled by federal actions. In a statement he issued he said, basically, in Oregon Oregon Law Enforcement is to abide by the laws of Oregon and the will of Oregon voters. He also stated these laws and these cards would not protect individuals from federal law or law enforcement. That individuals obtaining the cards and using and/or growing marijuana could be subject to federal arrest and prosecution. State cards were again issued.
Here in Oregon there's currently another fight between state and federal laws and agencies regarding assisted suicide.
Again, if it worked the way you're stating it does, there would be no reasons for these disagreements. State, county and local law enforcement agencies are not under the Executive Branch of the federal government. In fact in many municipalities local law enforcement agencies are not even under the executive branch of their local government, often they fall under the judicial branch.