The Egyptian Government has taken advantage of the irrational fear of Swine flu to slaughter the countries entire pig population. The majority of the pigs are raised by the poorest of the poor Christians to feed their families. This move will destroy the livlihoods of thousands. It is not surprising that they are using everything they can to stop the government from destroying what little they have.
The optics of the situation look like the government is taking an opportunity to prosecute the minority Christian population. The fact there is no scientific support that slaughtering the animals will help prevent spread of the flu in Egypt lends credibility to this theory.
Egypt has had their own problems dealing with Islamic fanatics. They have had terrorist attacks. They have been trying to stop terrorist organizations like Muslim Brotherhood. They have closed their border to Gaza out of fear that Hamas will get a foothold in Egypt. They have not demonstrated a desire to supress Christians to cater to these terrorist groups.
Egypt is well aware of what would happen if they do get a case of the Swine Flu. It would not take long for riots aimed at the Christian farmers. By destroying the pigs now they are appeasing those who would be angry at caring more about Christians then pigs. In the eyes of the violent ignorent they have been proactive at helping the situation.
If they get no cases of Swine all they have done is take away the livlihood of a forgotten segment of society that nobody really cares about. If there is a case, there will be no pigs to blame on the spread of the disease. They may prevent attacks against the farmers and possibly the right to raise pigs altogether. They have absolved themselves of blame from the group of society most likly to take advanatage of the situation to destabalize the government.
There is no logical health reason to slaughter the pig population. The government should have acted according to logic and reason to take the proper course of action to take real steps to protect the health of their citizens. If they really are looking ahead to worst case scenarios, their course of action may be wrong but does not seem as far fetched.