Tomatoes and sage are not antagonists, but I can imagine that if the tomatoes were shading the sage which likes to be high and dry and in full sun that could have caused your problem. Tomatoes and beans are not listed as companions, but they are not listed as antagonists either. If it works in your garden I say go for it.

Heavy givers like beans and peas, if they find in the soil, or have been inoculated with, the proper bacterium will collect nitrogen from the atmosphere and deposit it in nodes on their roots. These nodes are primarily for the plant while it is growing, but once it has been cut down those nodes rot into the soil and leave their nitrogen. So usually that sort of companion planting is over time as a rotation, but, Emilia Hazelip recommends always having some beans or peas growing, and that may be because part of what plants do to tease nutrients out of the soil for themselves is to leak some 25% of the nutrients they derive from gas exchanges and photosynthesis from their roots. Therefore, I can imagine that legumes may positively affect the growth of others nearby with the exception of those with whom they have an antagonistic relationship. It is a good idea to use many different types of beans and peas if you are constantly growing them.

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To respond to your question, I haven’t had trouble growing tomatoes in the same spot for a couple of years in a row. In fact, this year my tomatoes are better than ever. I think it’s the worm castings and other manure that you have provided that made a huge difference.

On the negative, my sage did really poorly near the tomatoes. I don’t know why, but I suspect it’s some sort of antagonistic relationship going on, not sure.

You say that heavy nitrogen feeders like lettuce tomatoes, squash, cucumbers, cabbage, and corn, do well to follow heavy nitrogen givers like beans and peas. What about planting them together? I have beans near my tomatoes. Do you think that helped?