I think every situation is quite unique. Whether you should run depends on various factors which include what your opponent has to gain from the attack, and what you have to gain from defending.
i.e. if it is someone attacking you for specific reasons (such as vandalising his car) they may persue you for quite some distance, whereas if they are attacking you to try and look tough, they will be very happy for you to run away.
If it is the local bully and you stand up to them, win or loose you may be able to deter his behaviour. Also, if you have a small child with you or slower associates, you may not be able to run from an attacker.
For me the question of running or not depends on whether aikido for you is just a self-defence or whether it is also Budo.