Works for me (see below). Please check that your server indeed uses (only) my.cnf which you have edited; the most common reason of such problems is that there is some other config file which overrides the one you think you are using.

elenst@ubuntu11:~/10.0.0-release$ cat 2.cnf
[mysqld]
default_storage_engine = MyISAM

elenst@ubuntu11:~/10.0.0-release$ bin/mysqld_safe --defaults-file=./2.cnf
130109 18:08:30 mysqld_safe Logging to '/home/elenst/10.0.0-release/data/ubuntu11.err'.
130109 18:08:31 mysqld_safe Starting mysqld daemon with databases from /home/elenst/10.0.0-release/data

elenst@ubuntu11:~/10.0.0-release$ bin/mysql -uroot
Welcome to the MariaDB monitor. Commands end with ; or \g.
Your MariaDB connection id is 1
Server version: 10.0.0-MariaDB MariaDB Server

Copyright (c) 2000, 2012, Oracle, Monty Program Ab and others.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

MariaDB [(none)]> select @@version;
----------------

----------------

----------------
1 row in set (0.00 sec)

MariaDB [(none)]> show variables like 'default_storage_engine';
------------------------------+

------------------------------+

------------------------------+
1 row in set (0.01 sec)

I will close it for now since it's not reproducible on my side.
Please feel free to re-open if you are still having it after checking that your cnf files are correct and there are no overriding settings either in other config files or on the command line. In this case please attach your complete cnf file, server error log since the last server startup, and output of SHOW GLOBAL VARIABLES command.
Thank you.