Anecdata: seems like internal pullups are usually 10s of kΩs, maybe 20-50kΩ. Most sensor boards that I see use 4.7kΩ, and work with 400KHz-1MHz "fast-mode+".
So 1kΩ is safe, but might be a bit on the aggressive side. At 3.3V, 1KΩ to ground burns 3.3mA, and there are two pull-ups per I2C bus.