Your question contains its answer. If I disagreed with you, it would necesserily mean that "too much spiritualisation" would be fine to me, which is absurd.
More seriously, how can you consider eliminating Ki from Aikido ? Do you want to bend it according to your own values ? Who is qualified enough to declare some "beliefs" dubious and some others certain ? You ? No matter how long you've been practising, you'll never have as much experience as O-sensei and his disciples, who consider Ki as one of the central elements of Aikido (the Way to Unite with Ki).
If you find many aspects of our art mysterious (as I do), maybe it's because things cannot be revealed at once and some remain hard to understand for a long time.