Are giant flares or storms in soft-gamma repeaters viable sources of gravitational radiation? Few theoretical studies have been concerned with this problem, with the small number using either highly idealized models or assuming a magnetic field orders of magnitude beyond what is supported by observations. We perform nonlinear general-relativistic magnetohydrodynamic simulations of large-scale hydromagnetic instabilities in magnetar models, which mimic the magnetic field reconfiguration expected in magnetar flares. We utilize these models to find gravitational-wave emission over a wide range of energies, from 1040 to 1047erg. This allows us to derive a systematic relationship between the surface field strength and the gravitational-wave strain. In particular, for typical magnetar fields of a few times 1015G, we conclude that a direct observation of f-modes excited by global magnetic field reconfigurations is unlikely with present or near-future gravitational-wave observatories, though we also discuss the possibility that modes in a low-frequency band up to 100 Hz could be sufficiently excited to be relevant for observation.