Hi it's best to remove the shrine, since Shugden is harmful to the Dharma. Even though your family is no longer following the path, it'll probably be best that there be as little connection as possible between your family and Shugden. Perhaps you could consider returning the shrine to the organization. Otherwise, as bohiruci sugg, perhaps you can seek advice from Charitable Assistance Society, or Amitabha Buddhist Centre.
Gelugpa is itself a school that is full of wisdom and skilful means. Unfortunately, many Shugden-associated orgs use names like "Chinese Gelugpa" or other common Buddhist names and start to confuse people. They also typically start off with teaching basic buddhism, then eventually intro the Shugden practice. In S'pore, currently the two known Shugden groups are "Gelugpa Buddhist Association (Singapore)" and "Oddiyana Buddhist Meditation Society". One should really try to keep one's path away from them.
You may read more information from HH Dalai Lama's office: http://www.dalailama.com/page.132.htm
Hope the above would be helpful for you.
May you and your family be continually guided by the Dharma.