I haven't watched those early episodes in ages, but I think any notions Mikey had of whacking Tony were mostly predicated on the fact that Junior and Tony were having conflict, and Mikey thought he might be able to parlay that into his own gains. I don't think Mikey's motivations for wanting to kill Tony were personal, as you say, but for reasons of business. Mikey is clearly a notch or two below Tony in terms of earning power and rank, but he has strong ambition of rising in rank, and eliminating Tony might help facilitate that.

Mikey certainly had ambitions of being Junior's right-hand and displacing Tony, but I don't see how this could be accomplished without Junior's support. If I remember correctly, Mikey tells his wife that Junior has plans to remove Tony, and this will help his own rise in the family. But then Junior begins to back-off on the idea and at that point I don't see how Mikey could be strong enough to go at it alone against Tony, and if he did, would that not anger Junior who had reconciled with Tony at that point?