Paul,
I don't see individual planets at 50% morale as a problem. They don't grow so their morale doesn't drop. At the beginning of a game I will even settle for some planets with 40% morale, these being planets that have not built their first social project. These are class 15 planets, so the higher class planets fare better in morale when I colonize them, and that helps my overall morale. As the game progresses and I get more social projects built, increase my production capability, get my economy going better, get the planets improved, etc., the morale of those planets goes up and they start growing. My overall morale might start below 60%, but by the time I research the first government switch this has improved to about 60%. I do not worry about loosing control of the senate as long as my overall morale doesn't drop below 57%.
In my current game (near to end game), my overall morale has grown to near 80% and I have many planets with morale that is constantly at 100%, and they have not yet reached max population that I can see. I also have star bases with mining upgrades built on many morale resources, which is helping as well by allowing me to colonize lower class planets. I have colonized just about every planet I can get of class 12 and up (I am now starting on class 11 planets, and it looks like I will be able to start on class 10s soon without much impacct on my overall morale).
I think the key here is to be willing to lower your standards at the start of a game in order to plan for the future. Don't try to keep a high morale value at the start. It detracts from your ability to expand and grow horizontally (that is, the number of colonies). This is a balancing act. You don't want to let your morale get dangerously low once your senate is established, but you want to keep your expansion rate as high as possible. Once you have colonized as many class 15+ planets as you can get you can put more effort into vertical growth and the big ticket morale improvers.
Speaking of this being a balancing act, don't forget that there are other factors to balance into this as well. One of them is military, and military defence is a difficult one to figure out. Most of my games I have been able to avoid building any ships to defend most of my planets. It all depends on where your empire starts in relation to other empires. Those where I started near the edge of the galaxy required less plenates defended than my current one where I started in the middle of the galaxy. It is possible to avoid war (until you are ready to initiate war) if you build defenders for only the planets within range of another race. Of course, this also requires that you are stronger in other areas as well, such as total population, techs researched, etc.. As I said, it is a balancing act. A VAST balancing act. And it takes a lot of study of how the AI reacts to what you do.