Well I think by only allowing half the teams make the tournament, it makes the regular season more meaningful ... you have to finish in the top half of the league to even get a shot. If you let all 8 in, then the regular season means less. With 8 in, the regular season only matters for seeding, which on a neutral court means very little. Other leagues do not invite every team to their tournament ... the MAC (also playing at a neutral site) only allows 8 of 12 teams to make its tourney.
For these 1 bid leagues, I actually think your idea of letting the regular season champ play the tourney champ is not a bad idea. Of course, that allows the regular season champ to take the conference tourney a bit less seriously knowing they always have one more shot.