It really does ruin the flow of the channel - it surely wouldn't be that hard to schedule the bulletins on the hour, half hour or during the back half hour when the channel is showing taped programming (I'm not sure if that's technically possible though).
The weekend schedules aren't set in stone anyway - Casualty, for example, hasn't got anything that even resembles a fixed time slot. So scheduling around the news would perhaps even make the schedules a bit more stable.
The Saturday schedule, for much of the year, is back timed to ensure Match of the Day starts at 2230. Assuming BBC One don't want a 30 minute Saturday news bulletin then MOTD would need to permanently start about ten minutes earlier. The early evening bulletin would be even harder to schedule - though I wonder if it would be possible to do one of the following:
a) Play out a recorded back half hour programme to BBC News Channel with BBC One in
studio E (different output from same studio to different channels)
b) Move BBC News to studio D for the early evening bulletin with London straight after - (London presenter would stand and would require very tight shots - same director etc. for network and London).
c) Move BBC News channel to studio D for the early evening bulletin and network bulletin and London both come from studio E - again London presenter standing with shared director etc. (I believe London has incredibly minimal staffing at weekends already).