I ride mostly western now. There are jumps up in both the arena and riding pasture where I board. It's not that big of a problem for me. I use them to train my horses. You can take down the poles and use them for trotting or lope overs. You can make a box to practice 360s in. You can add a rope to one and use it to train as a gate. Since you said the jumps are in the middle of the arena, there should be plenty of room to ride around the outside. Yes, I will agree that if you are training for barrel/flags/poles etc, the jumps will be in the way. But if you are not, why not try to make them useful?
"SUCCESS is not what horse you have . . . but what you do with that horse."