I am writing this assuming you are in the US. I have no idea what educational entrance requirements exist for homeschooled students elsewhere in the world. As a public and private high school teacher, it is my understanding that even homeschool parents must submit a "transcript" of sorts to colleges their children are applying to. A quick search online yields several tools for homeschool parents to use in creating these for their children, and, from what I understand, these transcripts must include not only their child's grades but also the curricula or textbooks the student used in their studies. This way, colleges and universities know that Sally's science curriculum wasn't entirely comprised of science fiction novels and re-runs of Star Trek the Next Generation. What this means for you is that if you are ONLY homeschooled for your senior year, you will probably still be required to submit a transcript for the previous 3 years of high school as your homeschool transcript would be incomplete. So colleges are going to see your GPA one way or another.
The advice you've been given to speak with individual admission counselors is absolutely the best so far. Every school is different and attempting to apply a definite statement to your situation is impractical. I would assume that, at this point, you know where you are most interested in attending college and it would behoove you to schedule some on-campus visits to speak directly with their admissions counselors. This way, you can address your specific concerns and get honest answers from them. You should also consider that colleges have minimum GPA requirements for their in-coming freshmen. If your GPA isn't high enough, they may not even look at your application. Truthfully, as Karl Bielefeldt pointed out, the high school students I have taught who have gone on to college have begun the process at the end of their junior years. If you've been attending public schools, I'm a little shocked you didn't know this all ready as this puts you significantly behind the eight-ball. Many colleges have their in-coming freshmen all ready locked in by mid-winter. I know I received my college acceptance letters all before Christmas of my senior year.
Typically, students who are highly intelligent but have low grades are classified as "underachieving" students. This could throw up a HUGE red flag for admissions counselors. College drop-out rates are pretty high right now. According to a Harvard study released in 2011, almost half of all American college students drop out before actually receiving an undergraduate degree. Schools might not be willing to gamble on a student they fear will only drop out or flunk out because he/she is unwilling to do the work. It makes their bottom line look bad, and, despite the fact that this is academia we're talking about, colleges and universities are all politics and business.
At this point, your best option for colleges may be to attend a community college for a couple of years just to get your GPA up. From my experiences, it seems that four-year colleges and universities are more willing to work with students who have accepted that maybe they didn't make the best decisions in high school and who have put in the effort and time needed to correct those decisions.
Having said that, I know that there were a few kids I went to undergrad with who were homeschooled in high school, and I believe at least a couple of them got in based on portfolios they had created of their work as well as ACT/SAT scores. If you've been trying to present at academic conferences, you might be able to include that work into a portfolio you create of your senior year.
At this point, I don't know that it necessarily matters which way you choose to go. Any damage your low GPA is going to do is all ready done and you probably won't be able to hide it. If you choose to go back into public school, you really need to spend the year focusing on getting better grades. If you choose to homeschool, there's nothing wrong with continuing your studies the way you see fit as long as you ensure that you complete all academic requirements necessary to receive a high school diploma from your state.
Your best bet is to take this messy GPA thing and really be able to discuss with admissions counselors what you've learned from the experience and how you've changed your behavior to reflect that. This might be as simple as taking some classes on time management and study skills.