Daniel Avery and K Thor Jensen wrote an article on Newsweek concerning three Jehovah’s Witnesses (JW)  - Paulos Eyasu, Isaac Mogos and Negede Teklemariam  - who have been mercilessly incarcerated since 1994 for refusing to take part in military service which is part of their pacifist beliefs..
Paulos Eyasu, Isaac Mogos and Negede Teklemariam—have been incarcerated in the Eritrea since 1994

Why can't the government allow them to take part in an alternative civilian service group to fulfil their obligation?

The JW’s doctrine of political neutrality has led to imprisonment of members who refused conscription.  Their members do not observe holidays they believe to have pagan origins, such as Christmas, Easter, and birthdays. They do not salute the national flag or sing the national anthem, and they refuse military service.

In Eritrea, the government stripped Jehovah's Witnesses of their civil and political rights in post-independence Eritrea.  They had the rights to live and work peacefully before independence.  After independence life changed for JW members rather harshly overnight.  JW members lost their political and social rights in their communities, their ID cards were promptly repossessed, their livelihoods severely compromised during the 1992 referendum, and they labelled s ‘enemy of the people’ became victims of media propaganda.

Members of all ages have been arrested for participating in religious meetings. On 24 September 1994, youngsters who refused to take part in National Service were arrested, imprisoned without trial, and remain imprisoned.

According to Human Rights Watch there are over 50 JW prisoners in Eritrea.  There could be more because the government does not disclose information on prisoners. HRW also reported that some JW prisoners died in prison.  

Visit Newsweek in order to read the most recent story on the Jehova’s Witnesses of Eritrea.