As for what grounds? The unlawful imprisonment and torture of a US citizen.
This is reason to prosecute those responsible for his detention and cause for lenience in sentencing, not for pardoning him before his trial has even fully started. If he were to receive an excessive sentence and either fail or be denied appeal, then a pardon may be justified.
EDIT: Thinking about this, I'm not sure a full pardon is right. Some form of clemency or commutation of the sentence may be more suited, such as reducing a custodial sentence in light of his previous treatment.
I'd also make certain that any evidence gained through that treatment be suppressed, although that's largely irrelevant here.
Going back to my example above of a murder suspect abused by police, such mistreatment can't always override guilt. I do think taking it into consideration when prescribing punishment makes sense, although I still feel a little uncomfortable treating it as an actual part of the punishment rather than mitigating circumstances.
For an extreme version, take the KSM case. He was waterboarded and held in far more degrading and abusive conditions than Manning. The things done to him during his early detention should never be part of the US's legal apparatus. We should never treat it as part of his punishment and should, frankly, find a way to prosecute those that put him through it. We should also not let it stop us prosecuting him to the fullest and fairest extent of the law, preferably ending with assigning him three thousand life sentences.
And just for the record, if I were the judge in his case? I'd go for a discoverable discharge, time served,
maybe a two-five year sentence based on what he was actually found guilty of, full medical expense coverage for life on the taxpayer dime and relocation to anywhere in the US or UK (he has the option of UK citizenship) he chooses.