I think it's reasonable to ask a question about usage, and the answer is no, native speakers would not normally say '*agree the verb.'
'Make the verb agree,' on the other hand, is perfectly normal; I can't think how else you would say it. That is, we usually use 'agree' to refer to singular/plural agreement, making one verb agree with the subject; one subject can have more than one verb, or you could be talking about the verbs of several sentences, but it's not what you think of first. For several verbs, like in a long description, I would be more inclined to say something like 'keep all the verbs in the same tense' or 'keep the verbs consistent.'
On the question of whether 'agree' can be transitive at all, we've established in past discussions, and it's clear from the dictionary, that it can in BE, but not in AE, where we agree on something.