I don't think Tom could've been a liability to Vito for the simple reason that the Don is ultimately the decision maker when it comes to Family matters. As a consigliere, Tom can offer his advice and counsel to the Don, but the decision ultimately lies with the Don. If the consigliere acts as a cut out for the Don, the orders he delivers come from the Don. Most definitions of the title indicate that the consigliere has no direct line authority of his own; he serves the Don directly and that's it.

Vito wasn't exactly overrun with choices for the position after Genco became terminally ill. Clemenza or Tessio would've been good choices save for the facts that Vito likely had no one to replace them in their current position, and appointing one over the other could potentially lead to feelings of discord between the one who was chosen and the one who wasn't.

Vito was attempting to groom Sonny for the Donship, so he was out (and I think he was serving as a sort of underboss anyway). It'd be hard for him to serve Vito effectively while he's stuck thinking about Lucy Mancini. Fredo was...well, Fredo. Michael was off fighting in the war at the time, assuming he would've even been slightly interested. Vito was also quite loathe to involve Michael in the Family business anyway.

That leaves...Tom. As we know, Tom is a well educated, intelligent lawyer who's still wet behind the ears. The novel indicates that Tom had only been the interim consigliere for three months. Vito wasn't long on choices, but Tom (in spite of his ancestry) was the best choice he had. He had a man who could overcome the prejudices against Italians, who could effectively represent the Family in the legal arena, and a loyal to the end man who could be taught.

I think Vito's plan was to bring Tom on as a green consigliere to an experienced, seasoned Don in himself. Vito would've felt that his Sicilian cunning and experience would be enough to cover for a green advisor until Tom came up to speed. Vito would then step away from the Donship and turn it over to Sonny. In that way, Sonny as the now green Don would be working with an experienced consigliere in Tom. Tom would be able to counsel him effectively in his role and offer useful advice.

Vito's plan for succession hit a snag when Vito was ambushed and secondly when Michael took over. All of this happened before Vito could get Tom the experience that he needed to serve as an effective advisor. Sonny the newly minted green Don plus Tom the green consigliere was a no win combination for either of them. Tom did the best he knew how, but it wasn't good enough.

When Michael took over the Donship, either he realized the scenario for himself or Vito pointed it up: Michael, for all of his assuredness, master plan and poise, was still a green Don. Tom was still the green consigliere. Less so than before, but still green. Tom was able to put the pieces together on Michael's master plan, including the existence of Rocco's secret regime, so he wasn't at all naive. He just didn't have the experience needed to guide the new Don through war.

Michael (and Vito) knew that, so "Tom was out". Not because he was a bad consigliere, but because his serving in that role would've been premature. Michael needed an experienced advisor, someone who had been there and done that. Enter Vito. When the war was over, Tom was right back in his old seat even if not formally reappointed.