Estou suspeitando de um bug no arquivo de controle apt ou mediawiki. O mediawiki precisa do apache2 ou do httpd instalado. O APT prefere o primeiro pacote e, se não estiver disponível, passa para o próximo, mas, neste caso, o próximo é um pacote virtual httpd, que também é fornecido pelo apache2-bin. Eu presumo que isso confunda com o apt que decide instalar o apache2 apenas para jogar com segurança.
Isso pode ser resolvido de duas maneiras, você pode dizer de uma maneira explícita que não deseja instalar o apache:
➜ ~ apt-get -s install nginx-extras mediawiki apache2-bin-
NOTE: This is only a simulation!
apt-get needs root privileges for real execution.
Keep also in mind that locking is deactivated,
so don't depend on the relevance to the real current situation!
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package 'apache2-bin' is not installed, so not removed
The following extra packages will be installed:
libdbd-mysql-perl libjs-jquery-cookie libjs-jquery-form libjs-jquery-tipsy
libluajit-5.1-2 libluajit-5.1-common libonig2 libqdbm14 mediawiki-classes
mediawiki-extensions-base mysql-client-5.5 mysql-server mysql-server-5.5
mysql-server-core-5.5 nginx-common php-wikidiff2 php5 php5-cgi php5-cli
php5-json php5-mysql php5-readline ssl-cert
Suggested packages:
imagemagick php5-gd mediawiki-extensions-math memcached clamav tinyca
fcgiwrap nginx-doc php-pear openssl-blacklist
The following NEW packages will be installed:
libdbd-mysql-perl libjs-jquery-cookie libjs-jquery-form libjs-jquery-tipsy
libluajit-5.1-2 libluajit-5.1-common libonig2 libqdbm14 mediawiki
mediawiki-classes mediawiki-extensions-base mysql-client-5.5 mysql-server
mysql-server-5.5 mysql-server-core-5.5 nginx-common nginx-extras
php-wikidiff2 php5 php5-cgi php5-cli php5-json php5-mysql php5-readline
ssl-cert
0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded.
Inst libluajit-5.1-common (2.0.3+dfsg-3 Debian:testing [all])
Inst libluajit-5.1-2 (2.0.3+dfsg-3 Debian:testing [amd64])
Inst libonig2 (5.9.5-3.1 Debian:testing [amd64])
Inst libdbd-mysql-perl (4.028-2+b1 Debian:testing [amd64])
Inst mysql-client-5.5 (5.5.40-1 Debian:testing [amd64])
Inst mysql-server-core-5.5 (5.5.40-1 Debian:testing [amd64])
Inst mysql-server-5.5 (5.5.40-1 Debian:testing [amd64])
Inst php5-mysql (5.6.4+dfsg-1 Debian:testing [amd64])
Inst libqdbm14 (1.8.78-5+b1 Debian:testing [amd64])
Inst php5-json (1.3.6-1 Debian:testing [amd64])
Inst php5-cli (5.6.4+dfsg-1 Debian:testing [amd64])
Inst php5-readline (5.6.4+dfsg-1 Debian:testing [amd64])
Inst libjs-jquery-cookie (10-1 Debian:testing [all])
Inst libjs-jquery-form (10-1 Debian:testing [all])
Inst libjs-jquery-tipsy (10-1 Debian:testing [all])
Inst nginx-common (1.6.2-5 Debian:testing [all])
Inst nginx-extras (1.6.2-5 Debian:testing [amd64])
Inst php5-cgi (5.6.4+dfsg-1 Debian:testing [amd64])
Inst php5 (5.6.4+dfsg-1 Debian:testing [all])
Inst mediawiki-classes (1:1.19.20+dfsg-2.2 Debian:testing [all])
Inst mediawiki (1:1.19.20+dfsg-2.2 Debian:testing [all])
Inst mediawiki-extensions-base (3.7 Debian:testing [all])
Inst mysql-server (5.5.40-1 Debian:testing [all])
Inst php-wikidiff2 (1.2+git03ea59f-1 Debian:testing [amd64])
Inst ssl-cert (1.0.35 Debian:testing [all])
Conf libluajit-5.1-common (2.0.3+dfsg-3 Debian:testing [all])
Conf libluajit-5.1-2 (2.0.3+dfsg-3 Debian:testing [amd64])
Conf libonig2 (5.9.5-3.1 Debian:testing [amd64])
Conf libdbd-mysql-perl (4.028-2+b1 Debian:testing [amd64])
Conf mysql-client-5.5 (5.5.40-1 Debian:testing [amd64])
Conf mysql-server-core-5.5 (5.5.40-1 Debian:testing [amd64])
Conf mysql-server-5.5 (5.5.40-1 Debian:testing [amd64])
Conf php5-mysql (5.6.4+dfsg-1 Debian:testing [amd64])
Conf libqdbm14 (1.8.78-5+b1 Debian:testing [amd64])
Conf php5-json (1.3.6-1 Debian:testing [amd64])
Conf php5-cli (5.6.4+dfsg-1 Debian:testing [amd64])
Conf php5-readline (5.6.4+dfsg-1 Debian:testing [amd64])
Conf libjs-jquery-cookie (10-1 Debian:testing [all])
Conf libjs-jquery-form (10-1 Debian:testing [all])
Conf libjs-jquery-tipsy (10-1 Debian:testing [all])
Conf nginx-common (1.6.2-5 Debian:testing [all])
Conf nginx-extras (1.6.2-5 Debian:testing [amd64])
Conf php5-cgi (5.6.4+dfsg-1 Debian:testing [amd64])
Conf php5 (5.6.4+dfsg-1 Debian:testing [all])
Conf mediawiki-classes (1:1.19.20+dfsg-2.2 Debian:testing [all])
Conf mediawiki (1:1.19.20+dfsg-2.2 Debian:testing [all])
Conf mediawiki-extensions-base (3.7 Debian:testing [all])
Conf mysql-server (5.5.40-1 Debian:testing [all])
Conf php-wikidiff2 (1.2+git03ea59f-1 Debian:testing [amd64])
Conf ssl-cert (1.0.35 Debian:testing [all])
ou você pode relatar um bug para o pacote mediawiki pedindo que a dependência do apache2 seja removida, já que ele já está listado como provedor do pacote virtual httpd, e nesse caso ele deve resolver o problema.
Sempre que você não quiser que um pacote seja instalado, você pode acrescentar menos -
ao nome do pacote que você não deseja instalar, e o apt irá respeitá-lo, como visto no exemplo.