It's not a ridiculous argument. Arguably, the case was not sufficiently ripe for the courts until Henderson's arbitration ruling was handed down. As a general matter, litigants are expected to exhaust their remedies under arbitration proceedings provided by a CBA before turning to the courts.
The difficulty for the NFL is three-fold: 1. Judge Mazzant convincingly found that the wrong in this case was a procedural wrong (failure by Henderson to admit evidence that the CBA required be admitted) that was independent of and didn't need to wait for the outcome of Henderson's decision; 2. Mazzant also properly pointed out that the injunction remedy is intended to prevent damage before it occurs -- in this case, the remedy would have been rendered useless if Zeke waited for the outcome of Henderson's decision since the damage would have been done (particularly as it would have allowed the NFL to control timing and jurisdiction of seeking court confirmation of Henderson's decision); and 3. the NFL undercut its position by filing the appeal with the 5th circuit before Mazzant had rendered his decision (giving the appearance that its complaint is tactical rather than principled).